Ok so I am re-analysing some publicly available chip-seq data (human H3K4me3 & H3K27me3) and have a few questions
at the moment my "pipeline" is to align reads with bowtie (using --best), convert to maq format and generate .wigs & peaks with findpeaks
Comparing to the publication, I am mapping 29M/40M reads, where they only mapped ~9M so i believe they are throwing out reads which map equally well to multiple places in the genome, whereas bowtie is reporting a random sampling of the best alignments (ala maq).
does anyone have thoughts on which way is better to go for chip-seq peak finding?
at the moment my "pipeline" is to align reads with bowtie (using --best), convert to maq format and generate .wigs & peaks with findpeaks
Comparing to the publication, I am mapping 29M/40M reads, where they only mapped ~9M so i believe they are throwing out reads which map equally well to multiple places in the genome, whereas bowtie is reporting a random sampling of the best alignments (ala maq).
does anyone have thoughts on which way is better to go for chip-seq peak finding?
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