How to recover the entire sequence from all_contig_annotations.csv?
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4 weeks ago

After processing the scTCR-seq or scBCR-seq data using cellranger, I discovered that the concatenated sequence of any contig (fwr1+cdr1+fwr2+cdr2+fwr3+cdr3+fwr4), extracted from the all_contig_annotations.csv, is shorter than the sequence in all_contig.fasta. Specifically, it appears that all_contig_annotations.csv excludes the first fragment of the fasta sequence.

My question is, if I only have access to the all_contig_annotations.csv and don't have the raw data, but I require the complete sequence to perform igblastn, is there a method to recover the entire sequence from all_contig_annotations.csv? Thanks in advance.

VDJ single-cell TCR-seq cellranger 10x • 119 views
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