BaDoi Phan
BaDoi Phan
The command I used was the following. I'll check but I remember that 10x only had 1 ATAC barcode list, which is the list I provided. The issue first is...
Thanks I'll run with that parameter. I tried aligning over the weekend with K=15 and W=7 and got a lower map rate, so I'll try to go for higher K'...
Hi all, I reached out to 10x and they advised that some sequencers provide the reverse complement of the barcodes, so I made a rev-comp whitelist. I get more hits...
The initial runs were with an index built w/ K17 W7, which produced very low map rates.
Now that you mentioned all of that, I think I get the error now. I aligned w/ the default index k17 w7, with the reverse complement barcode list and looks...
I finished trying this version of the peak calling + reproducible peak clustering and completed without any errors. Shouldn't change underlying peak calling by grabbing the replicate summits from `narrowPeakFile`...
That makes sense. The https://github.com/macs3-project/MACS/blob/master/docs/callpeak.md#output-files says they should be the same, but on my files, I found the scores in `summits.bed` and `peaks.narrowPeak` are off by a factor of 10....
Thanks Ryan! I'm working on identifying which metrics of open chromatin that are comparable across bulk ATAC, pseudo-bulk ATAC, and single-cell aggregated peak accessibility--especially for the ML sequence prediction models....
You'll have to update R and bio conductor versions. I have R v3 and going to R v4 did the trick.
Please open up a new ticket with the GitHub managers. I am a user.