jcohn42

I found this thread when troubleshooting run times for jobs that I had running, where MACS2 was part of an analysis pipeline to process ChIPseq data. I looked at the...

A follow up regarding this issue - I found that I get different results with different files. I tested pre-processed BED files from SRA - also ChIPseq data, and macs2...

@taoliu, yes that is right, the SRA data does have many chromosomes (10 maize chromosomes and a few dozed contigs). They are present in the pre-processed BED files downloaded from...

@taoliu The files come from https://www.ncbi.nlm.nih.gov/bioproject/PRJNA492464 GSM3397995 Chip B73 leaf H3K56ac rep1 SRR7889772 GSM3398001 Chip B73 leaf input rep1 SRR7889778 Here is my macs3 call with the processed BED files...

@taoliu, can you clarify if the problem you described was 'fixed' "The process hangs at p-q table calculation is an old issue I dealt with years ago where when the...

@taoliu I discovered the problem - it was an issue with my genome size input - a typo! Thanks again for your replies; btw, MACS3 is also working quite well...

update - after some troubleshooting; I think I may understand what is happening: if "gene_name" is available, this will be added to "gene_id", so prepde output will be "gene_id|gene_name". If...