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Aurélien Ginolhac
snakemake-chip-seq
Commits
75f1069c
Verified
Commit
75f1069c
authored
Jul 09, 2021
by
Aurélien Ginolhac
🚴
Browse files
add one unit for one sample
parent
252e1123
Changes
2
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config/config.yaml
View file @
75f1069c
...
...
@@ -4,7 +4,7 @@
samples
:
"
config/samples.tsv"
# The source of fastq files for every sequencing unit of all samples has to be provided in the units.tsv file.
units
:
"
config/units.tsv"
single_end
:
Fals
e
single_end
:
Tru
e
resources
:
ref
:
...
...
@@ -44,18 +44,18 @@ params:
# when activated the plot profile and heatmap plot are generated, this involves a matrix calculation that requires a lot of working memory.
activate
:
False
lc_extrap
:
activate
:
Tru
e
activate
:
Fals
e
picard_metrics
:
activate
:
True
deseq2
:
# set to True to use the vst transformation instead of the rlog transformation for the DESeq2 analysis
vst
:
False
peak-annotation-analysis
:
activate
:
Tru
e
activate
:
Fals
e
peak-qc
:
activate
:
True
consensus-peak-analysis
:
activate
:
Tru
e
activate
:
Fals
e
# samtools view parameter suggestions (for full parameters, see: https://www.htslib.org/doc/samtools-view.html):
# if duplicates should be removed in this filtering, add "-F 0x0400" to the params
# if for each read, you only want to retain a single (best) mapping, add "-q 1" to params
...
...
config/units.tsv
View file @
75f1069c
...
...
@@ -2,5 +2,6 @@ sample unit fq1 fq2 sra_accession platform
A 1 data/single_end_test_data/A-1_chr21.fastq.gz ILLUMINA
B 1 data/single_end_test_data/B-1_chr21.fastq.gz ILLUMINA
C 1 data/single_end_test_data/C-1_chr21.fastq.gz ILLUMINA
C 2 data/single_end_test_data/C-2_chr21.fastq.gz ILLUMINA
D 1 data/single_end_test_data/D-1_chr21.fastq.gz ILLUMINA
E 1 data/single_end_test_data/E-1_chr21.fastq.gz ILLUMINA
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