Commit a292efcb authored by Nikola de Lange's avatar Nikola de Lange

changed description regarding paired-end mode, removed mkdir, instructions to...

changed description regarding paired-end mode, removed mkdir, instructions to create an new directory
parent e2202d9f
......@@ -105,7 +105,6 @@
samtools sort -n - > SRR891268.bam
# Peak Calling
mkdir
Genrich -t SRR891268.bam -o SRR891268.narrowPeak \
-e "chrM" -f SRR891268.log -m 30 -j\
......@@ -113,9 +112,9 @@
-k SRR891268.bg
```
* 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.
* 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 we had in the previous data set from the tutorial) other parameters are needed for the alignment with `bowtie2`.
`-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.\
`Genrich` has an advantage over `MACS2` since it is offering to do the necessary filtering steps during 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.\
......@@ -125,6 +124,12 @@
*
* Write the script into a Snakefile.
* Create a new directory `atac-seq` in your home directory for this (see the code below)
```bash
$ cd
$ mkdir atac-seq
$ cd atac-seq
```
* The peak caller `Genrich` is available from the `bioconda` conda channel
2. How can you improve the workflow in the context of data management? Think about data structures and log files.
......
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