The samples file used for this run:
| sample |
assembly |
descriptive_name |
control |
| SRR1528625 |
hg38 |
KC1_p63 |
SRR1528616 |
| Dombi-23_unsure_p63_chip |
hg38 |
KC2_p63 |
|
| PRIM2_LSC_unsure_p63_chip |
hg38 |
LSC1_P63 |
PRIM_LSC_input |
| PRIM_LSC_p63_chip |
hg38 |
LSC2_P63 |
PRIM_LSC_input |
| GSM4728087 |
hg38 |
LSC1_RUNX1 |
PRIM_LSC_input |
| GSM4728088 |
hg38 |
LSC2_RUNX1 |
PRIM_LSC_input |
| GSM4728089 |
hg38 |
LSC1_PAX6 |
PRIM_LSC_input |
| GSM4728090 |
hg38 |
LSC2_PAX6 |
PRIM_LSC_input |
| GSM4728091 |
hg38 |
LSC1_SMAD3 |
PRIM_LSC_input |
| GSM4728092 |
hg38 |
LSC2_SMAD3 |
PRIM_LSC_input |
The config file used for this run:
# tab-separated file of the samples
samples: samples.tsv
# pipeline file locations
result_dir: ./results # where to store results
genome_dir: ../genomes # where to look for or download the genomes
fastq_dir: ../fastq_dir # where to look for or download the fastqs
# contact info for multiqc report and trackhub
email: Jsmits@science.ru.nl
# produce a UCSC trackhub?
create_trackhub: True
# how to handle replicates
biological_replicates: fisher # change to "keep" to not combine them
technical_replicates: merge # change to "keep" to not combine them
# which trimmer to use
trimmer: fastp
# which aligner to use
aligner: bwa-mem
# filtering after alignment
remove_blacklist: True
min_mapping_quality: 30
only_primary_align: True
# peak caller
peak_caller:
macs2:
--keep-dup 1 --buffer-size 10000