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I have mapped FAIRE-seq data with paired end reads. The read counts don't seem to "match" up to my expectations and it was recommended that I try to "fill in" the pairs and map/count those alignments rather than just the reads which represent the two ends of the library strand.
Even if you don't know what FAIRE is (it's a method to map open-chromatin sites genome-wide using differential formaldehyde crosslinking), if my description makes sense to you and you know of a program or method that could do it for me, let me know. The reads are already mapped and I've been visualizing in IGV, so maybe I can use IGV or something similar to make a track where the bar covers the space between the two pairs.
Even if you don't know what FAIRE is (it's a method to map open-chromatin sites genome-wide using differential formaldehyde crosslinking), if my description makes sense to you and you know of a program or method that could do it for me, let me know. The reads are already mapped and I've been visualizing in IGV, so maybe I can use IGV or something similar to make a track where the bar covers the space between the two pairs.
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