aligning 5' seq with - white list file

Question

[kanwarjag]

I want to align 10x sequencing file with whitelist of barcode for quality checks. The reason I want to do is as running ranger or Starsolo does not extract any bar code. What should be the best approach to extract 28 bp from Fastq and find the part of sequence in whitelist?

Thanks

Answer 1

[Kevin Blighe]

I provide information for barcodes here: STARsolo config for 10x Chromium v1, v2, v3

Also, STARsolo can indeed identify barcodes for you if you perform an alignment and use --soloCBwhitelist None.

UMItools can also help to identify barcodes: https://umi-tools.readthedocs.io/en/latest/reference/whitelist.html#

Kevin