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how to handle the UMI sequence of Immune Repertoire sequencing .fastq data

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fastp immune repertoire ir-seq pandaseq sequencing umi
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written by Yuki _ISHIKAWA • Yuki _ISHIKAWA

Ideally, details about the reads, like UMI length and position, should be described in the paper and/or BioProject. But if the authors didn't give enough metadata to actually make use of their deposited data (sure wouldn't be the first time) you might have to nag them. Can you share any accession numbers?

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written by Jesse • Jesse

The accession numbers is PRJNA390125(Project consists of 46 subjects). Thanks!

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written by Yuki _ISHIKAWA • Yuki _ISHIKAWA

Is it possible there just aren't UMIs here at all? Taking the first sample (SRX2912165) as an arbitrary example it says:

Alpha chain TCR transcripts running from 5' of reverse transcription reaction to beginning of constant region, produced by merging R1 and R2 reads.

So it sounds like the sequences they uploaded span from however much of the V segment is included in each cDNA molecule down through the end of J and just before C. Nothing about extra barcoding.

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written by Jesse • Jesse

Thank you for your response. I used MiXCR to get the CDR3 sequences ,and confirmed it works.

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written by Yuki _ISHIKAWA • Yuki _ISHIKAWA

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