Skip to content

Commit

Permalink
Update README.md
Browse files Browse the repository at this point in the history
  • Loading branch information
jojdavies authored Feb 18, 2021
1 parent bd39dc4 commit 2c1d1b2
Showing 1 changed file with 6 additions and 0 deletions.
6 changes: 6 additions & 0 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -91,3 +91,9 @@ You can then run the second part of the pipe by changing the initial parts from
The options gzip, postgzip, clean_wig and samtobam allow you to compress and clean up the files quickly

The macs2 option will call MACS2 for simple peak calling

The MCC_pipe2.pl script creates temporary scripts called align_tmp.sh in each of the folders created by the first part of the pipeline.
The align_tmp.sh is overwritten for each of the targets so you will only see the commands for the last target.
Be careful running this command - it is worthwhile testing this part of the pipeline on one set of files first (easy to do by hashing out the file= in the MCC_pipe_config.txt) otherwise it will potentially try to execute hundreds of jobs simultaneously (e.g. 6 replicates with 100 targets = 600 jobs).


0 comments on commit 2c1d1b2

Please sign in to comment.