Commit e2202d9f authored by Nikola de Lange's avatar Nikola de Lange

Parameters removed from Genrich and description of remaining parameters

parent da2cec95
......@@ -96,24 +96,34 @@
# Build the bowtie index of the reference for the mapping
bowtie2-build chr22.fa.gz hg38_chr22
# Mapping
bowtie2 -x hg38_chr22 -1 SRR891268_R1.fastq.gz -2 SRR891268_R2.fastq.gz \
-I 0 -X 500 --fr --dovetail --very-sensitive | \
# Alignment
bowtie2-build chr22.fa.gz hg38_chr22
bowtie2 -x hg38_chr22 -1 SRR891268_R1.fastq.gz -2 SRR891268_R2.fastq.gz | \
samtools sort -n - > SRR891268.bam
# Peak Calling
Genrich -t SRR891268.bam -o SRR891268.narrowPeak \
-e "chrM" -f SRR891268.log -m 0 -j -d 100\
-q 0.05 -a 20 -l 0 -g 100 -v \
-e "chrM" -f SRR891268.log -m 30 -j\
-a 20 -r \
* Atac-seq is similar to ChIP-seq an epigenomics NGS technique to identify open chromatin. Since the sequencing is in a paired-end mode (instead of single-end like ChIP-seq) other parameters are needed for the alignment.
`-1` indicates the forward read while `-2` indicates the reverse read.\
`Genrich` has an advantage over `MACS2` since it is offering to do necessary filtering steps during the peak calling.\
`-e` allows to exclude chromosomes that are specified. In this case the mitochondrial chromosome (chrM). \
`-m` filters low quality reads. \
`-j` specifies that it has to run in the atac-seq mode.\
`-a` is the minimum AUC for a peak\
`-r` removes PCR duplicates.\
`-k` creates a bedgraph-ish file for pileups. \
* Write the script into a Snakefile.
* The peak caller `Genrich` is available from the `bioconda` conda channel
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