Example 1. Working with the output of MACS in the UCSC genome browser.
Before, let us assume that we have run MACS to find the peaks of one sample, using a second sample as a control:
> macs14 -t H2AUb1_Pombo.bam -c ControlIP_Pombo.bam -g mm -n H2AUb1_Pombo -B -S --nomodel --shiftsize 75
MACS, after running the previous command, has generated the BedGraph profile of the ChIPseq experiment:
However, when we upload this profile in UCSC (mm9), we realize that something is wrong:
We run SeqCode for processing and cleaning this BedGraph file in mm9:
> bin/processmacs -v ChromInfo.txt H2AUb1_Pombo_treat_afterfiting_all.bdg.gz H2AUb1_Pombo_nocompact.bdg H2AUb1_Pombo
The new profile generated by SeqCode is correctly uploaded into the UCSC genome browser interface:
Example 2. Generating compact profiles that require a lower amount of space.
Now, we run SeqCode for processing and cleaning this BedGraph file in mm9 using the option -c:
> bin/processmacs -cv ChromInfo.txt H2AUb1_Pombo_treat_afterfiting_all.bdg.gz H2AUb1_Pombo.bdg H2AUb1_Pombo
When comparing to the previous profile, we see the performance of the reduction operation in the file size:
The profile generated by SeqCode is correctly uploaded into the UCSC genome browser interface: