User: sonark

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sonark10
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3 months ago
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2 years, 7 months ago
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a*******@ku.edu.tr

Posts by sonark

<prev • 3 results • page 1 of 1 • next >
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Answer: A: GSEA after MACS2 peak calling for ChIP-seq; want positive enrichment only
... *** . **Update:** I have found that the best & easiest option is to use the "[**Investigate Gene Sets**][1]" page on the **GSEA MSigDB website** where you can compute overlaps of your gene list with MSigDB gene sets (up to 2026 genes allowed). It provides a P value based on "[**Hypergeometric ...
written 7 months ago by sonark10
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GSEA after MACS2 peak calling for ChIP-seq; want positive enrichment only
... 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 ...
macs2 chip-seq gsea written 9 months ago by sonark10
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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. ...
written 2.6 years ago by sonark10

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