Commit 2453fe64 authored by Tommy Tang's avatar Tommy Tang
Browse files

explain downsampling target_reads

parent 9d9174a1
......@@ -9,6 +9,7 @@ Now, this is working on LSF, I will have another branch for SLURM.
![](./GEO_rulegraph.png)
In the `config.yaml` file you can change settings. e.g. path to a different genome to align, p value cut-offs. The `target_reads` is the number of reads that downsampled to. I set 15 million for default. If the number of reads of the orignal bam files are less than `target_reads`, the pipeline will just keep whatever the number it has.
### Dependiencies
......@@ -135,7 +136,7 @@ Rscript ../scripts/sraDownload.R -a 'ascp -QT -l 300m -i ~/.aspera/connect/etc/a
`chmod u+x download.sh`
```bash
# inside the GEOpyflow-ChIPseq folder:
# inside the GEOpyflow-ChIPseq/01seq folder:
cat ../SRR.txt | sed '1d' | tr "\t" "\n" | sort | uniq > srr_unique.txt
## only have 4 jobs in parallel, good behavior on a cluster
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment