Commit bb8d1f45 authored by Sarah Peter's avatar Sarah Peter

Some formatting adjustments

parent e99160d5
......@@ -89,6 +89,7 @@
## Shell script into Snakefile
1. Have a look at the following shell script.
The script is adapted from the first few steps of the Galaxy atac-seq tutorial (https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/atac-seq/tutorial.html)
```bash
......@@ -112,17 +113,21 @@
-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 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 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.\
`-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.
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 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.
* `-a` is the minimum AUC for a peak.
* `-r` removes PCR duplicates.
* `-k` creates a bedgraph-ish file for pileups.
2. Write the script into a Snakefile.
* Create a new directory `atac-seq` in your home directory for this (see the code below)
```bash
$ cd
......@@ -130,6 +135,6 @@
$ 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.
3. How can you improve the workflow in the context of data management? Think about data structures and log files.
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