search

YeoLab / eCLIP

Other
38 stars 26 forks source link

What‘s the colnames of peakClusters.normed.compressed.bed? #41

Closed FionaMoon closed 1 year ago

FionaMoon commented 1 year ago

Hi eCLIP group, I've run the last step —— input normalization of eclip data. I finally get 3 files:

peakClusters.normed.bed peakClusters.normed.bed.full *peakClusters.normed.compressed.bed

*peakClusters.normed.compressed.bed file like this:

chrY 10200210 10200258 1.94901389247387 2.3362390115803 + chr1 161531127 161531166 400 4.6478251622462 + chr1 109100490 109100500 400 3.25080353507424 + chr1 109100302 109100309 400 3.24763099942376 + chr1 109100474 109100482 400 3.20977101024239 + chr1 109100452 109100473 400 2.83631261471494 + chr1 109100331 109100339 400 2.71000603798728 + ...

I've find the colnames of *bed.full files in your documents: image

However, I can't find discriptions about *peakClusters.normed.compressed.bed file.

FionaMoon commented 1 year ago

Inaddtation, I would like to view the difference between control/treatment group by IGV. I don't know which file should be the input of IGV. Is that ok to use the following files?

peakClusters.normed.compressed.bed input.NIL.r1.fq.genome-mappedSo.rmDupSo.r2.bam

Or I should use the bw files?

Treat_replicates_genome-mappedSo.rmDupSo.merged.r2.norm.neg.bw Control_input.NIL.r1.fq_genome-mappedSo.rmDupSo.merged.r2.norm.neg.bw