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liulab-dfci / TRUST4

TCR and BCR assembly from RNA-seq data
MIT License
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No overlap between the barcodes from TRUST4 and those in the barcodes.tsv.gz #233

Open ChangLu92 opened 11 months ago

ChangLu92 commented 11 months ago

I downloaded a patient's scrna count raw data as well as the scVDJ, scRNA sequence data from GEO, and ran './run-trust4 -f human_IMGT+C.fa --ref human_IMGT+C.fa -u xxx_r2.fastq.gz --barcode xxx_r1.fastq.gz --readFormat bc:0:15,um:16:-1 -o result' for both scRNA and scVDJ sequence. However, I found very limited overlap between the barcodes generated by TRUST4 and the barcodes in the barcodes.tsv.gz I downloaded from GEO. Do you know what the problem is? Thanks a lot!

mourisl commented 11 months ago

Can you check whether the barcode is reverse-complemented? How many shared clonotypes do you see overlap between scRNA and scVDJ, just to make sure they are from the same sample.