Searching tool to convert MACS output (chr + coordinates) into genomic feature

[SS Santos]

Hi I'm curating a database and I'm having trouble with a paper with ChIP-seq raw data. I have the MACS output for peak calling and the corresponding "target genes", but I'm only interested in peaks that fall within gene promoters, and that is not indicated. Is there a tool that, when I use the full MACS output, or only the chromosome / start / end columns, tells me where that sequence interval falls?

Please help!


The format is like this:

chr start end length summit tags -10*log10(pvalue) fold_enrichment FDR(%)
chr01.fs 20885 20948 64 31 28 76.41 5.85 52.94
chr01.fs 62827 62973 147 83 55 61.56 3.14 68.85

[charlesli]

You're basically looking to do peak annotation. I've used Homer (http://biowhat.ucsd.edu/homer/ngs/annotation.html) in the past, but I'm sure other options exist.

[paolo.kunder]

Hi,

Package ChIPpeakAnno of Bioconductor could help you lo locate your peaks along the genome,

http://www.bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html

or you could just use http://nebula.curie.fr/root and annotate your peak list,

Paolo

[ai_seq]

Homer error

You're basically looking to do peak annotation. I've used Homer (http://biowhat.ucsd.edu/homer/ngs/annotation.html) in the past, but I'm sure other options exist.

When you use Homer, did you meet this problem?

Preparing HTML output with sequence logos...
1 of 215 (1e-395) Foxa2(Forkhead)/Liver-Foxa2-ChIP-Seq/Homer
ESP Ghostscript 815.02: Unrecoverable error, exit code 1
2 of 215 (1e-341) FOXA1(Forkhead)/LNCAP-FOXA1-ChIP-Seq/Homer
ESP Ghostscript 815.02: Unrecoverable error, exit code 1

....
The error does not happen every time just sometimes. Do you know what is happened to it? Thanks a lot!

[ai_seq]

Homer error

You're basically looking to do peak annotation. I've used Homer (http://biowhat.ucsd.edu/homer/ngs/annotation.html) in the past, but I'm sure other options exist.

Did you use Homer for motif analysis?

For motif analysis using by Homer, did you get this error?

Preparing HTML output with sequence logos...
1 of 215 (1e-395) Foxa2(Forkhead)/Liver-Foxa2-ChIP-Seq/Homer
ESP Ghostscript 815.02: Unrecoverable error, exit code 1
2 of 215 (1e-341) FOXA1(Forkhead)/LNCAP-FOXA1-ChIP-Seq/Homer
ESP Ghostscript 815.02: Unrecoverable error, exit code 1

....
The error does not happen every time just sometimes. Do you know what is happened to it? Thanks a lot!

[ai_seq]

Homer

You're basically looking to do peak annotation. I've used Homer (http://biowhat.ucsd.edu/homer/ngs/annotation.html) in the past, but I'm sure other options exist.

Did you use Homer for motif analysis?

I got a problem when I use homer for motif analysis. Do you know what is happened to it? Thanks a lot!

Preparing HTML output with sequence logos...
1 of 215 (1e-395) Foxa2(Forkhead)/Liver-Foxa2-ChIP-Seq/Homer
ESP Ghostscript 815.02: Unrecoverable error, exit code 1
2 of 215 (1e-341) FOXA1(Forkhead)/LNCAP-FOXA1-ChIP-Seq/Homer
ESP Ghostscript 815.02: Unrecoverable error, exit code 1

....
The error does not happen every time just sometimes.