Open danledinh opened 2 years ago
oh that is weird. the format for fastq read names should be @CellBarcode_UMI#OriginalName. so there should be only one cell barcode and UMI tag in the read name. can you give me the original fastq read so I can identify what is wrong? Is this the only read that have long name or it is the same for all reads?
Unfortunately, I can't release the FASTQ per company policy. Here are some more observations that might help you troubleshoot the problem:
1) I used an edit distance of 2 2) About 10-15% of BC-matched reads have more than 1 BC/UMI appended 3) The multiple BC/UMI reads are mostly at the end of the FASTQ file (is there a sorting step?)
I hope that helps!
Minimap2/Samtools is throwing an error from reads with append cell barcode/UMI (generated from
match_cell_barcode
).Here is an example qname:
Looks like qname must be equal to or shorter than 254 characters: https://github.com/samtools/samtools/issues/1081