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HorvathLab / NGS

Next-Gen Sequencing tools from the Horvath Lab
https://horvathlab.github.io/NGS/
MIT License
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scReadCount: -G option #1

Closed vbruat closed 3 years ago

vbruat commented 3 years ago

Hi,

I'm trying to use scReadCount but the barcode of the cell in my bam is in the CB tag. I don't know how to specify this in the advanced -G option. Example: A00469:88:HNL2KDMXX:2:1209:31476:14231 16 1 14658 255 98M * 0 0 CAAGTCTGGGTCTGGGGGGGAAGGTGTCATGGAGCCCCCTACGATTCCCAGTCGTCCTCGTCCTCCTCTGCCTGTGGCTGCTGCGGTGGCGGCAGAGG -FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF CB:Z:GCTGCGAAGATCTGCT-1 UB:Z:ACATTGACTT RE:A:I PG:Z:MarkDuplicates RG:Z:CPTP_0012:0:1:HNL2KDMXX :2 NH:i:1 HI:i:1 nM:i:0 CR:Z:GCTGCGAAGATCTGCT UR:Z:ACATTGACTT AS:i:96 CY:Z:FFFFFFFFF:FFFFFF UY:Z::FFFFFFFFF xf:i:0 li:i:0

Thanks.

edwardsnj commented 3 years ago

The provide options for the cell-barcode (aka read grouping) are: STARsolo and UMI-tools. Turns out, the STARsolo grouping is what you need. Its definition (in the group.ini file) is:

[STARsolo]
Description: Cell barcodes added by STARsolo in CB tag in aligned read, reads without a CB tag dropped.
ReadTagValue: tag='CB'

If you'd like to provide a value for reads without a CB tag (instead of dropping them) or use your own name for the grouping strategy:

[MyBarcodes]
Description: Cell barcodes from my BAM file.
ReadTagValue: tag='CB' missing='CBMISSING'

in a file group.ini in the working directory where you run SCReadCounts (you can change group.ini in the distribution, but you might overwrite it with a new release).

Specify: -G STARsolo or -G MyBarcodes

Let me know if this doesn't do what you need!

Cheers!

vbruat commented 3 years ago

Hi, Thanks for answering me quickly, I've tried the option -G STARsolo but I get the following error:

Traceback (most recent call last): File "scReadCounts.py", line 169, in NameError: name 'readgropup' is not defined [6655] Failed to execute script scReadCounts

edwardsnj commented 3 years ago

Sorry about that. You must be on release 1.1.3 or earlier, that was fixed in release 1.1.4. You should find this problem goes away with the most recent release.

vbruat commented 3 years ago

You're right, I changed to version 1.1.4 and it works!

Thank you!!!