MultiQC Report

A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

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Report generated on 2025-03-28, 14:45 CET based on data in:

/scratch/siebrenf/lore4/qc/general_stats.tsv
/scratch/siebrenf/lore4/qc/reads_per_step.tsv
/scratch/siebrenf/lore4/qc/skera.tsv
/scratch/siebrenf/lore4/qc/lima.tsv
/scratch/siebrenf/lore4/qc/isoseq_correct_barcodes.tsv
/scratch/siebrenf/lore4/qc/isoseq_correct.tsv
/scratch/siebrenf/lore4/qc/isoseq_bcstats.tsv
/scratch/siebrenf/lore4/qc/isoseq_collapse.tsv
/scratch/siebrenf/lore4/qc/pigeon_classify_classifications_by_read.tsv
/scratch/siebrenf/lore4/qc/pigeon_classify_classifications.tsv
/scratch/siebrenf/lore4/qc/pigeon_classify_rt_switching.tsv
/scratch/siebrenf/lore4/qc/pigeon_classify_genes.tsv
/scratch/siebrenf/lore4/qc/pigeon_classify_filter_reasons.tsv
/scratch/siebrenf/lore4/qc/pigeon_classify_classifications_by_cell.tsv
/scratch/siebrenf/lore4/qc/pigeon_classify_classifications_by_transcript.tsv
/scratch/siebrenf/lore4/qc/pigeon_classify_classifications_by_isoform.tsv
/scratch/siebrenf/lore4/qc/pigeon_classify_classifications_by_mapping.tsv
/scratch/siebrenf/lore4/qc/pigeon_classify_junctions.tsv
/scratch/siebrenf/lore4/qc/pigeon_report.tsv
/scratch/siebrenf/lore4/qc/segmented.knee_mqc.png
/scratch/siebrenf/lore4/pbmm2/segmented.stats.tsv
/scratch/siebrenf/lore4/pbmm2/segmented.coverage.tsv
/scratch/siebrenf/lore4/pbmm2/segmented.bam.mtnucratiomtnuc.json
/scratch/siebrenf/lore4/qc

General Statistics

Showing ¹/₁ rows and ⁷/₂₁ columns.

Sample Name	Reads in cells	% Reads in cells	MT genome coverage	Genome coverage	MT to Nuclear Ratio	M Genome reads	M MT genome reads	Error rate	Non-primary	Reads mapped	% Mapped	% Proper pairs	% MapQ 0 reads	Total seqs	Mean insert	Reads	Bases	Coverage	Mean depth	Mean BQ	Mean MQ
segmented	25.5M	28.0%	21562.0X	5.2X	4139.3	16.0M	0.4M	0.47%	0.0M	16.2M	99.6%	0.0%	8.4%	16.3M	0.0bp	16.4M	570.4Mb	18.4%	5.1x	38.7	54.9

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: general_stats_table_table

Sort	Group	Column	Description	ID	Scale
\|\|	Custom content: general_stats	Reads in cells	Number of barcoded, full-length non-concatemer reads in cells (Millions)	`custom_content_general_stats-m_reads`
\|\|	Custom content: general_stats	% Reads in cells	Percentage of barcoded, full-length non-concatemer reads in cells	`custom_content_general_stats-reads`
\|\|	mtnucratio	MT genome coverage	Average coverage (X) on mitochondrial genome.	`mtnucratio-mt_cov_avg`
\|\|	mtnucratio	Genome coverage	Average coverage (X) on nuclear genome.	`mtnucratio-nuc_cov_avg`
\|\|	mtnucratio	MT to Nuclear Ratio	Mitochondrial to nuclear reads ratio (MTNUC)	`mtnucratio-mt_nuc_ratio`
\|\|	mtnucratio	M Genome reads	Reads on the nuclear genome (millions)	`mtnucratio-nucreads`	read_count
\|\|	mtnucratio	M MT genome reads	Reads on the mitochondrial genome (millions)	`mtnucratio-mtreads`	read_count
\|\|	Samtools: stats	Error rate	Error rate: mismatches (NM) / bases mapped (CIGAR)	`samtools_stats-error_rate`
\|\|	Samtools: stats	Non-primary	Non-primary alignments (millions)	`samtools_stats-non_primary_alignments`	read_count
\|\|	Samtools: stats	Reads mapped	Reads mapped in the bam file (millions)	`samtools_stats-reads_mapped`	read_count
\|\|	Samtools: stats	% Mapped	% Mapped reads	`samtools_stats-reads_mapped_percent`
\|\|	Samtools: stats	% Proper pairs	% Properly paired reads	`samtools_stats-reads_properly_paired_percent`
\|\|	Samtools: stats	% MapQ 0 reads	% of reads that are ambiguously placed (MapQ=0)	`samtools_stats-reads_MQ0_percent`
\|\|	Samtools: stats	Total seqs	Total sequences in the bam file (millions)	`samtools_stats-raw_total_sequences`	read_count
\|\|	Samtools: stats	Mean insert	Average insert size	`samtools_stats-insert_size_average`
\|\|	Samtools: coverage	Reads	Total number of mapped reads	`samtools_coverage-numreads`	read_count
\|\|	Samtools: coverage	Bases	Total number of mapped base pairs	`samtools_coverage-covbases`	base_count
\|\|	Samtools: coverage	Coverage	Percentage of region covered with reads	`samtools_coverage-coverage`
\|\|	Samtools: coverage	Mean depth	Mean depth of coverage	`samtools_coverage-meandepth`
\|\|	Samtools: coverage	Mean BQ	Mean base quality	`samtools_coverage-meanbaseq`
\|\|	Samtools: coverage	Mean MQ	Mean mapping quality	`samtools_coverage-meanmapq`

Reads per processing step

The number of reads remaining after each processing step. The final reads are deduplicated and aligned to the genome/transcriptome.

Legend:
ccs_reads: Circular consensus sequencing (HiFi) reads (Skera)
s_reads: Segmented reads (Skera)
primed_reads: Primed reads (Lima)
fl_reads: Full Length reads (Iso-seq correct)
flnc_reads: Full Length Non-Chimeric reads (Iso-seq correct)
polya_reads: PolyA-tailed reads (Iso-seq correct)
non-missing: Barcoded reads (Iso-seq correct)
yield_reads: Estimated reads in cells (Iso-seq correct).

Created with MultiQC

Skera

Deconcatenates Kinnex HiFi reads to produce S-reads that represent the original cDNA molecules.

Showing ¹/₁ rows and ⁵/₅ columns.

sample	reads	s_reads	mean_len_s_reads	percent_full_array	mean_array_size
segmented	6104086.0	91323074.0	981.0	87.5	15.0

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: skera-section-plot_table

Sort	Column	Description	ID
\|\|	reads	Reads	`reads`
\|\|	s_reads	Segmented Reads (S-Reads)	`s_reads`
\|\|	mean_len_s_reads	Mean Length of S-Reads	`mean_len_s_reads`
\|\|	percent_full_array	Percentage of Reads with Full Array	`percent_full_array`
\|\|	mean_array_size	Mean Array Size (Concatenation Factor)	`mean_array_size`

Lima

Removes and spurious false positives.

Showing ¹/₁ rows and ¹⁵/₁₅ columns.

sample	Reads input	Reads above all thresholds (A)	Reads below any threshold (B)	(B) Below min length	(B) Below min score	(B) Below min end score	(B) Below min passes	(B) Below min score lead	(B) Below min ref span	(B) Without SMRTbell adapter	(B) Wrong different pair	(B) Undesired 5p--5p pairs	(B) Undesired 3p--3p pairs	(A) With same pair	(A) With different pair
segmented	91323074	90692203	630871	12350	0	228466	6	0	490179	0	0	192404	231319	0	90692203

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: lima-section-plot_table

Sort	Column	Description	ID
\|\|	Reads input	Reads input	`Reads_input`
\|\|	Reads above all thresholds (A)	Reads above all thresholds (A)	`Reads_above_all_thresholds_A`
\|\|	Reads below any threshold (B)	Reads below any threshold (B)	`Reads_below_any_threshold_B`
\|\|	(B) Below min length	(B) Below min length	`B_Below_min_length`
\|\|	(B) Below min score	(B) Below min score	`B_Below_min_score`
\|\|	(B) Below min end score	(B) Below min end score	`B_Below_min_end_score`
\|\|	(B) Below min passes	(B) Below min passes	`B_Below_min_passes`
\|\|	(B) Below min score lead	(B) Below min score lead	`B_Below_min_score_lead`
\|\|	(B) Below min ref span	(B) Below min ref span	`B_Below_min_ref_span`
\|\|	(B) Without SMRTbell adapter	(B) Without SMRTbell adapter	`B_Without_SMRTbell_adapter`
\|\|	(B) Wrong different pair	(B) Wrong different pair	`B_Wrong_different_pair`
\|\|	(B) Undesired 5p--5p pairs	(B) Undesired 5p--5p pairs	`B_Undesired_5p_5p_pairs`
\|\|	(B) Undesired 3p--3p pairs	(B) Undesired 3p--3p pairs	`B_Undesired_3p_3p_pairs`
\|\|	(A) With same pair	(A) With same pair	`A_With_same_pair`
\|\|	(A) With different pair	(A) With different pair	`A_With_different_pair`

Iso-seq correct

Identifies cell barcode errors and corrects them. Additionally, Iso-seq correct estimates which reads are likely to originate from real cells vs ambrient RNA.

Stats

Showing ¹/₁ rows and ¹⁰/₁₀ columns.

sample	processed_reads	filtered_reads	processed_bases	edit_read_count	unchanged_read_count	missing_read_count	found_but_failing_read_count	failing_read_count	yield_count	yield_fraction
segmented	90460688.0	0.0	80744625524.0	90448488.0	4241.0	7959.0	64935802.0	64943761.0	25516927.0	0.3

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: isoseq_correct_stats-plot_table

Sort	Column	Description	ID
\|\|	processed_reads	processed_reads	`processed_reads`
\|\|	filtered_reads	filtered_reads	`filtered_reads`
\|\|	processed_bases	processed_bases	`processed_bases`
\|\|	edit_read_count	edit_read_count	`edit_read_count`
\|\|	unchanged_read_count	unchanged_read_count	`unchanged_read_count`
\|\|	missing_read_count	missing_read_count	`missing_read_count`
\|\|	found_but_failing_read_count	found_but_failing_read_count	`found_but_failing_read_count`
\|\|	failing_read_count	failing_read_count	`failing_read_count`
\|\|	yield_count	yield_count	`yield_count`
\|\|	yield_fraction	yield_fraction	`yield_fraction`

Barcode corrections

Created with MultiQC

Barcode stats

Showing ¹/₁ rows and ¹⁰/₁₀ columns.

sample	number_unique_groupbarcodes	number_unique_molbarcodes	total_number_reads	mean_groupbarcode_depth	cutoff_threshold	number_of_cells	median_umis_per_cell	reads_in_cells	fraction_reads_in_cells	mean_reads_per_cell
segmented	1589554.0	67814241.0	90460688.0	56.0	1306.0	13880.0	2491.0	57572148.0	0.6	4147.0

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: isoseq_bcstats-plot_table

Sort	Column	Description	ID
\|\|	number_unique_groupbarcodes	Number of Unique Cell/Group Barcodes	`number_unique_groupbarcodes`
\|\|	number_unique_molbarcodes	Number of UMIs	`number_unique_molbarcodes`
\|\|	total_number_reads	Number of Reads	`total_number_reads`
\|\|	mean_groupbarcode_depth	Mean Group Barcode Depth	`mean_groupbarcode_depth`
\|\|	cutoff_threshold	Frequency Cutoff	`cutoff_threshold`
\|\|	number_of_cells	Number of Cells	`number_of_cells`
\|\|	median_umis_per_cell	Median UMIs Per Cell	`median_umis_per_cell`
\|\|	reads_in_cells	Total Number of Reads in Cells	`reads_in_cells`
\|\|	fraction_reads_in_cells	Fraction Reads In Cells	`fraction_reads_in_cells`
\|\|	mean_reads_per_cell	Mean Reads per Cell	`mean_reads_per_cell`

Knee plots

Samtools

Version:


                      
                        1.21

Toolkit for interacting with BAM/CRAM files.URL: http://www.htslib.orgDOI: 10.1093/bioinformatics/btp352

Percent mapped

Alignment metrics from samtools stats; mapped vs. unmapped reads vs. reads mapped with MQ0.

For a set of samples that have come from the same multiplexed library, similar numbers of reads for each sample are expected. Large differences in numbers might indicate issues during the library preparation process. Whilst large differences in read numbers may be controlled for in downstream processings (e.g. read count normalisation), you may wish to consider whether the read depths achieved have fallen below recommended levels depending on the applications.

Low alignment rates could indicate contamination of samples (e.g. adapter sequences), low sequencing quality or other artefacts. These can be further investigated in the sequence level QC (e.g. from FastQC).

Reads mapped with MQ0 often indicate that the reads are ambiguously mapped to multiple locations in the reference sequence. This can be due to repetitive regions in the genome, the presence of alternative contigs in the reference, or due to reads that are too short to be uniquely mapped. These reads are often filtered out in downstream analyses.

Created with MultiQC

Alignment stats

This module parses the output from samtools stats. All numbers in millions.

Created with MultiQC

Sample Name	Total sequences	Mapped & paired	Properly paired	Duplicated	QC Failed	Reads MQ0	Mapped bases (CIGAR)	Bases Trimmed	Duplicated bases	Diff chromosomes	Other orientation	Inward pairs	Outward pairs
segmented	16.3M	0.0M	0.0M	0.0M	0.0M	1.4M	15677.3Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: samtools-stats-dp_table-1

Sort	Column	Description	ID	Scale
\|\|	Total sequences	Total sequences	`raw_total_sequences`	read_count
\|\|	Mapped & paired	Paired-end technology bit set + both mates mapped	`reads_mapped_and_paired`	read_count
\|\|	Properly paired	Proper-pair bit set	`reads_properly_paired`	read_count
\|\|	Duplicated	PCR or optical duplicate bit set	`reads_duplicated`	read_count
\|\|	QC Failed	QC Failed	`reads_QC_failed`	read_count
\|\|	Reads MQ0	Reads mapped and MQ=0	`reads_MQ0`	read_count
\|\|	Mapped bases (CIGAR)	Mapped bases (CIGAR)	`bases_mapped__cigar`	base_count
\|\|	Bases Trimmed	Bases Trimmed	`bases_trimmed`	base_count
\|\|	Duplicated bases	Duplicated bases	`bases_duplicated`	base_count
\|\|	Diff chromosomes	Pairs on different chromosomes	`pairs_on_different_chromosomes`	read_count
\|\|	Other orientation	Pairs with other orientation	`pairs_with_other_orientation`	read_count
\|\|	Inward pairs	Inward oriented pairs	`inward_oriented_pairs`	read_count
\|\|	Outward pairs	Outward oriented pairs	`outward_oriented_pairs`	read_count

Coverage: global stats

Stats parsed from samtools coverage output, and summarized (added up or weighted-averaged) across all regions.

Showing ¹/₁ rows and ⁶/₆ columns.

Sample Name	Reads	Bases	Coverage	Mean depth	Mean BQ	Mean MQ
segmented	16.4M	570.4Mb	18.4%	5.1x	38.7	54.9

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: samtools-coverage-table_table

Sort	Column	Description	ID	Scale
\|\|	Reads	Total number of mapped reads	`numreads`	read_count
\|\|	Bases	Total number of mapped base pairs	`covbases`	base_count
\|\|	Coverage	Percentage of region covered with reads	`coverage`
\|\|	Mean depth	Mean depth of coverage	`meandepth`
\|\|	Mean BQ	Mean base quality	`meanbaseq`
\|\|	Mean MQ	Mean mapping quality	`meanmapq`

Coverage: stats per region

Per-region stats parsed from samtools coverage output.

Created with MultiQC

Iso-seq collapse

Collapses redundant transcripts into unique isoforms based on exonic structures.

Showing ¹/₁ rows and ²/₂ columns.

sample	number_mapped_unique_isoforms	number_of_mapped_unique_loci
segmented	367493	66670

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: isoseq_collapse-section-plot_table

Sort	Visible	Group	Column	Description	ID	Scale
\|\|			number_mapped_unique_isoforms	number_mapped_unique_isoforms	`number_mapped_unique_isoforms`
\|\|			number_of_mapped_unique_loci	number_of_mapped_unique_loci	`number_of_mapped_unique_loci`

Pigeon Classify

Pigeon is used to classify isoforms into categories, filter this output, and to report on the gene and isoform- level saturation.

Classifications overview

Showing ²/₂ rows and ⁵/₅ columns.

Sample	Input	Passed	Removed	Unique genes	Unique transcripts
segmented	367145	None	None	194323	334597
segmented (filtered)	367145	99229	267916	18466	73051

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: pigeon_classify_classification-plot_table

Sort	Column	Description	ID
\|\|	Input	Input	`Input`
\|\|	Passed	Passed	`Passed`
\|\|	Removed	Removed	`Removed`
\|\|	Unique genes	Unique genes	`Unique_genes`
\|\|	Unique transcripts	Unique transcripts	`Unique_transcripts`

Classifications by read

Showing ²/₂ rows and ⁹/₉ columns.

Sample	Full splice match	Incomplete splice match	Novel in catalog	Novel not in catalog	Antisense	Genic intron	Genic genomic	Intergenic	Other
segmented	281708	277377	43298	87264	69017	642	214816	631518	2711
segmented (filtered)	272569	178479	41068	35980	2359	0	1211	4518	1514

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: pigeon_classify_classification_by_read-plot_table

Sort	Column	Description	ID
\|\|	Full splice match	Full splice match	`Full_splice_match`
\|\|	Incomplete splice match	Incomplete splice match	`Incomplete_splice_match`
\|\|	Novel in catalog	Novel in catalog	`Novel_in_catalog`
\|\|	Novel not in catalog	Novel not in catalog	`Novel_not_in_catalog`
\|\|	Antisense	Antisense	`Antisense`
\|\|	Genic intron	Genic intron	`Genic_intron`
\|\|	Genic genomic	Genic genomic	`Genic_genomic`
\|\|	Intergenic	Intergenic	`Intergenic`
\|\|	Other	Other	`Other`

Classifications by isoform

Showing ²/₂ rows and ⁹/₉ columns.

Sample	Full splice match	Incomplete splice match	Novel in catalog	Novel not in catalog	Antisense	Genic intron	Genic genomic	Intergenic	Other
segmented	23132	40877	19057	45211	23068	139	48061	166177	1423
segmented (filtered)	22714	32325	18155	19999	1490	0	725	2969	852

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: pigeon_classify_classification_by_isoform-plot_table

Sort	Column	Description	ID
\|\|	Full splice match	Full splice match	`Full_splice_match`
\|\|	Incomplete splice match	Incomplete splice match	`Incomplete_splice_match`
\|\|	Novel in catalog	Novel in catalog	`Novel_in_catalog`
\|\|	Novel not in catalog	Novel not in catalog	`Novel_not_in_catalog`
\|\|	Antisense	Antisense	`Antisense`
\|\|	Genic intron	Genic intron	`Genic_intron`
\|\|	Genic genomic	Genic genomic	`Genic_genomic`
\|\|	Intergenic	Intergenic	`Intergenic`
\|\|	Other	Other	`Other`

Classifications by cell

Showing ²/₂ rows and ⁴/₄ columns.

Sample	median_genes_per_cell	median_transcripts_per_cell	median_genes_per_cell_known	median_transcripts_per_cell_known
segmented	205.0	210.0	117.0	70.0
segmented (filtered)	76.0	78.0	75.0	64.0

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: pigeon_classify_classification_by_cell-plot_table

Sort	Column	Description	ID
\|\|	median_genes_per_cell	median_genes_per_cell	`median_genes_per_cell`
\|\|	median_transcripts_per_cell	median_transcripts_per_cell	`median_transcripts_per_cell`
\|\|	median_genes_per_cell_known	median_genes_per_cell_known	`median_genes_per_cell_known`
\|\|	median_transcripts_per_cell_known	median_transcripts_per_cell_known	`median_transcripts_per_cell_known`

Classifications by transcript

Showing ²/₂ rows and ⁴/₄ columns.

Sample	transcripts_fsm	transcripts_ism	transcripts_nic	transcripts_nnc
segmented	23132.0	40877.0	19057.0	45211.0
segmented (filtered)	22714.0	32325.0	18155.0	19999.0

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: pigeon_classify_classification_by_transcript-plot_table

Sort	Column	Description	ID
\|\|	transcripts_fsm	Transcripts classified as Full-splice Matches (FSM)	`transcripts_fsm`
\|\|	transcripts_ism	Transcripts classified as Incomplete-splice Matches (ISM)	`transcripts_ism`
\|\|	transcripts_nic	Transcripts classified as Novel In Catalog (NIC)	`transcripts_nic`
\|\|	transcripts_nnc	Transcripts classified as Novel Not In Catalog (NNC)	`transcripts_nnc`

Classifications by mapping

Showing ²/₂ rows and ³/₃ columns.

Sample	flnc_mapped_genome	flnc_mapped_transcriptome	flnc_mapped_transcriptome_excluding_ribomito
segmented	1608351.0	689647.0	658094.0
segmented (filtered)	537698.0	528096.0	499423.0

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: pigeon_classify_classification_by_mapping-plot_table

Sort	Column	Description	ID
\|\|	flnc_mapped_genome	flnc_mapped_genome	`flnc_mapped_genome`
\|\|	flnc_mapped_transcriptome	flnc_mapped_transcriptome	`flnc_mapped_transcriptome`
\|\|	flnc_mapped_transcriptome_excluding_ribomito	flnc_mapped_transcriptome_excluding_ribomito	`flnc_mapped_transcriptome_excluding_ribomito`

Junctions

Showing ²/₂ rows and ⁴/₄ columns.

Sample	Known canonical	Known non-canonical	Novel canonical	Novel non-canonical
segmented	643342	1966	54047	50036
segmented (filtered)	525443	42	39918	0

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: pigeon_classify_junctions-plot_table

Sort	Column	Description	ID
\|\|	Known canonical	Known canonical	`Known_canonical`
\|\|	Known non-canonical	Known non-canonical	`Known_non_canonical`
\|\|	Novel canonical	Novel canonical	`Novel_canonical`
\|\|	Novel non-canonical	Novel non-canonical	`Novel_non_canonical`

Genes

Showing ²/₂ rows and ²/₂ columns.

Sample	Known	Novel
segmented	18477	175846
segmented (filtered)	14336	4130

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: pigeon_classify_genes-plot_table

Sort	Visible	Group	Column	Description	ID	Scale
\|\|			Known	Known	`Known`
\|\|			Novel	Novel	`Novel`

RT Switching

Showing ²/₂ rows and ⁴/₄ columns.

Sample	All transcripts	Unique transcripts	All junctions	Unique junctions
segmented	16546	1034	17283	17283
segmented (filtered)	None	None	None	None

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: pigeon_classify_rt_switching-plot_table

Sort	Column	Description	ID
\|\|	All transcripts	All transcripts	`All_transcripts`
\|\|	Unique transcripts	Unique transcripts	`Unique_transcripts`
\|\|	All junctions	All junctions	`All_junctions`
\|\|	Unique junctions	Unique junctions	`Unique_junctions`

Filter reasons

Showing ²/₂ rows and ⁴/₄ columns.

Sample	Intrapriming	Monoexonic	RT switching	Low coverage/non-canonical
segmented	None	None	None	None
segmented (filtered)	23330	0	14550	230036

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: pigeon_classify_filter_reasons-plot_table

Sort	Column	Description	ID
\|\|	Intrapriming	Intrapriming	`Intrapriming`
\|\|	Monoexonic	Monoexonic	`Monoexonic`
\|\|	RT switching	RT switching	`RT_switching`
\|\|	Low coverage/non-canonical	Low coverage/non-canonical	`Low_coverage_non_canonical`

Saturation reports

Gene and isoform- level saturation. The tables show the number of unique genes found in a subsampled number of reads.

Created with MultiQC

Software Versions

Software Versions lists versions of software tools extracted from file contents.

Software	Version
Samtools	`1.21`
mtnucratio	`0.7.1`

v1.27.1

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About MultiQC

General Statistics

Reads per processing step

Skera

Lima

Iso-seq correct

Stats

Barcode corrections

Barcode stats

Knee plots

Samtools

Percent mapped

Alignment stats

Coverage: global stats

Coverage: stats per region

Iso-seq collapse

Pigeon Classify

Classifications overview

Classifications by read

Classifications by isoform

Classifications by cell

Classifications by transcript

Classifications by mapping

Junctions

Genes

RT Switching

Filter reasons

Saturation reports

Software Versions

Toggle navigation v1.27.1

MultiQC Toolbox

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Tool Citations

About MultiQC

General Statistics

General Statistics: Columns

Reads per processing step

Skera

Skera: Columns

Lima

Lima: Columns

Iso-seq correct

Stats

Stats: Columns

Barcode corrections

Barcode stats

Barcode stats: Columns

Knee plots

Samtools

Percent mapped Help

Alignment stats

Samtools: stats: Alignment Stats: Columns

Coverage: global stats

Samtools: coverage: Summary: Columns

Coverage: stats per region

Iso-seq collapse

Iso-seq collapse: Columns

Pigeon Classify

Classifications overview

Classifications overview: Columns

Classifications by read

Classifications by read: Columns

Classifications by isoform

Classifications by isoform: Columns

Classifications by cell

Classifications by cell: Columns

Classifications by transcript

Classifications by transcript: Columns

Classifications by mapping

Classifications by mapping: Columns

Junctions

Junctions: Columns

Genes

Genes: Columns

RT Switching

RT Switching: Columns

Filter reasons

Filter reasons: Columns

Saturation reports

Software Versions

v1.27.1

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Percent mapped