search

phbradley / conga

Clonotype Neighbor Graph Analysis
MIT License
79 stars 18 forks source link

conga.tcrdist.make_10x_clones_file.make_10x_clones_file #29

Closed afilaliM781 closed 2 years ago

afilaliM781 commented 2 years ago

Hello, I got an empty ab_counts when running conga.tcrdist.make_10x_clones_file.make_10x_clones_file using one 10X sample. No old_paired_barcodes detected as well as new_stringent_paired_barcodes

ab_counts: [] old_unpaired_barcodes: 2964 old_paired_barcodes: 0 new_stringent_paired_barcodes: 0 compute tcrdist distance matrix for 0 clonotypes Using C++ TCRdist calculator Read 0 paired tcrs from file MS.tmp_hs_pbmc_clones_AB.dist_50_kpcs_tcrs.tsv making MS.tmp_hs_pbmc_clones_AB.dist_50_kpcs_tcrdists.txt

Thanks for your Help

Ali

phbradley commented 2 years ago

Hi Ali, Thanks for giving conga a try! Is it possible that there aren't any cell barcodes with both alpha and beta TCR chains? Can you find any by eye, or by looking at the clonotypes file? Alternatively you could share a snippet of the contigs file, here or by email (pbradley@fredhutch.org) and we could help debug... Take care, Phil