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Posts by dariasc
... Hello, I have called histone modification ChIP-seq peaks compared to a control using MACS2 and annotated them using Homer. I then try to perform pre-ranked GSEA. I only have positive values in my ranking, but I also get negative enrichment so I think GSEA is treating the genes at the bottom of my l ...
Answer: A: samtools faidx error
... Instead of using samtools to create index file, you can use IGV; under Tools -> Run igvtools... then select Index and your genome fasta file or BAM file as the input. This will give you the .fai or .bai index file. ...
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