Expected barcodes for 10X Chromium data

[whitleyo]

Hi,

My input bam files come from a 10X Chromium experiment and have entries with format

GTTCCTCCAAGTCGATGGCACCTCCCTCCCTCTCAACCACTTGAG DADBCHII?FGE?DCGGEG1@<C1C?CGCHIH?FEHIHGHHDGHGHHHH<EFIHHHH<@GHHHHEHHHGHIEEHEHEEGH1C@H=EGHFC@EGEHEE?0C< NH:i:5 HI:i:2 AS:i:99 nM:i:0 RE:A:I BC:Z:CTGACTGA QT:Z:DDDADIIH CR:Z:GACACGCAGATGTTAG CY:Z:DDDDDIIIIGIIIIII CB:Z:GACACGCAGATGTTAG-1 UR:Z:TTGAATCTAC UY:Z:IIIIIGIIGH UB:Z:TTGAATCTAC RG:Z:945_I:MissingLibrary:1:HYMK5BCXY:2

CB indicates the cell barcode tag.

For the input barcodes for velocyto, I'm assuming that the input barcode should be formatted as GACACGCAGATGTTAG-1 and not GACACGCAGATGTTAG, correct? I've formatted the input barcodes as such for a test run of velocyto and there are only a few entries for which I get a warning that cell + umi barcode not found.

2019-06-28 17:21:49,870 - WARNING - Not found cell and umi barcode in entry 443 of the bam file
2019-06-28 17:21:49,870 - WARNING - Not found cell and umi barcode in entry 444 of the bam file
2019-06-28 17:21:49,871 - WARNING - Not found cell and umi barcode in entry 614 of the bam file
2019-06-28 17:21:49,873 - WARNING - Not found cell and umi barcode in entry 820 of the bam file
2019-06-28 17:21:49,874 - WARNING - Not found cell and umi barcode in entry 872 of the bam file
2019-06-28 17:21:49,874 - WARNING - Not found cell and umi barcode in entry 896 of the bam file
2019-06-28 17:21:49,875 - WARNING - Not found cell and umi barcode in entry 928 of the bam file

command: velocyto run -b $barcodes_file -o $new_dir -@ $threads $new_bam $gtf_file

Environment:

running on a cluster, so don't know which node the job is running on, but probably something like this Linux node62.uhnh4h.cluster 2.6.32-696.18.7.el6.x86_64 #1 SMP Thu Jan 4 17:31:22 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

Looking through my emails, it appears that all nodes are CentOS 6

Thanks!

[imilenkovic]

Hello! I have a similar problem, did you manage to solve it? Thanks!