dropEst ERROR: unable to parse out UMI
jhe2020 opened this issue · 4 comments
Hello, I'm trying dropEst on 10x 3' GEX v3.1 data for the first time. I'm getting unable to parse out UMI errors. I'm not sure what the problem is. Does the config file need to be modified? The input is a bam file from CellRanger count. Code is as follows. Thanks ahead of time for your help.
~/build/bin/dropest -m -F -L eiEIBA -o run1 -g ~/mm10/genes/genes.gtf -c ~/dropEst/configs/indrop_v3.xml ~/outs/possorted_genome_bam.bam
The configs file should be 10x.xml rather than indrop_v3.xml.
Also, if it is v3, then see also #90
I tried 10x.xml and specified <umi_length>12</umi_length>
But I still get the same errors
The data is from 10x v3.1
@mangospa I think you do not need to do additional barcode merge (-m), but this is my usage of dropEst. (I cannot find the exact thread in the issue section, but I remember there was a discussion about the UMI merge and cellranger is doing it reasonably).
(EDITED: Thank you @VPetukhov for the correction)
@mangospa When you run dropest only Estimation section of the config matters. So, umi_length doesn't play any role. Most probably the problem is in bam tags. Please check BamTag section in the config and ensure that tags in the config correspond to those in the bam.
@chlee-tabin , thanks for answering the question! Small correction: -m is the barcode merge, and -u is the UMI merge. Nevertheless, you're right and there is no reason to use it with 10x bam file.