10X fastq barcode+index and bam for Trust4

[olu2016]

Hi,

I have tcr fastq datasets, and the barcode+umi is 20bp (NCCCAAGGGT+AAAGGTAGTA) instead of the usual 26bp. I wondered if Trust4 could work successfully in this scenario?

Another question is: One of the bam files in the vdj_t folder (from cellranger multi pipeline) is consensus.bam, can Trust4 use this kind of bam file as input?

Thanks

[mourisl]

I have tcr fastq datasets, and the barcode+umi is 20bp (NCCCAAGGGT+AAAGGTAGTA) instead of the usual 26bp. I wondered if Trust4 could work successfully in this scenario?

Yes, the format should be fine. You just need to adjust the --readFormat option accordingly.

One of the bam files in the vdj_t folder (from cellranger multi pipeline) is consensus.bam, can Trust4 use this kind of bam file as input?

Is consensus.bam file already the result from cellranger's assembly? While TRUST4 can take it as input, I don't see the need for that. Do you mean you want to reannotate those cellranger's assemblies?

[olu2016]

Thanks for your reply. Yes, I just wanted the reannotation of the assemblies.

[mourisl]

It might not be directly supported, as the consensus.bam, is not the alignment to the reference genome, so the chromosome IDs will cause some issues. You may need to convert the BAM file to fastq file first.

[olu2016]

Thanks a lot. I used the raw data in fastq format and the 26 bp (barcode+format) format and my Trust4 run was successful. The 20 bp format that I earlier indicated was wrong.

Have a good day!