Samantha Klasfeld

@taoliu Thanks for getting back to me! What do you mean by the cut site? Would `--extsize 1` only use the 5' ends for modeling? Sorry, I just assumed the...

Okay, I understand now. Thank you for the response. The problem is that my read length is not uniform, but I guess I should just use the average length or...

Here are the broadpeak and xls files [version2.1.1.20160309_peaks.xls.txt](https://github.com/macs3-project/MACS/files/5329970/version2.1.1.20160309_peaks.xls.txt) [version2.2.7.1_peaks.xls.txt](https://github.com/macs3-project/MACS/files/5329966/version2.2.7.1_peaks.xls.txt) [version2.2.7.1_peaks.broadPeak.txt](https://github.com/macs3-project/MACS/files/5329967/version2.2.7.1_peaks.broadPeak.txt) [version2.1.1.20160309_peaks.broadPeak.txt](https://github.com/macs3-project/MACS/files/5329968/version2.1.1.20160309_peaks.broadPeak.txt)

You're welcome. Also when I continue down the pipeline, the b value for the wald-test is not output anymore. Does this have to do with having the aggregation_column?

Update: I realized that I need to sort all the 358 inputs and sort them. My result is closer to the one posted but it still does not match perfectly.

`if(miss < (binSize/binOverlap + 200)) { // bridge over adjacent bins plus 100 * 200 = 20kb` I am a bit confused about this part of the code. Since we...

I changed: "if(miss < (binSize/binOverlap + 200)) { // bridge over adjacent bins plus 100 * 200 = 20kb" to "if(miss < (binSize/binOverlap + 50)) { // bridge over adjacent...

I did notice that one of the mapped input files, ENCFF620WUR.bam, used to generate the blacklist is empty when I try to download it. Could this be causing the descrepancy?

Below are the inputs I used. I sort and index them using samtools and then run the blacklist tool. `1bda0787cf4d5cd51b9097242c871a57 ENCFF233VTH.bam ac0f8526cfb22439ae889b57b30d7768 ENCFF681BGF.bam c9bc2d5f89db104070238afe85ee2ed7 ENCFF732VPR.bam 8852656fdd8f95d79d306da6ebfb4e4a ENCFF077CZT.bam fbfc80c9d0faf591912bd4755dbb813d ENCFF147WIX.bam 134f826105b6ff8ff731d6865e75aa8f...

Yeah I just ended up using all the control bam files and letting MACS2 do the random down sampling.