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

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19 months ago

Yuki _ISHIKAWA ▴ 20

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fastp Immune Repertoire IR-SEQ pandaseq sequencing UMI • 791 views

ADD COMMENT • link 19 months ago by Yuki _ISHIKAWA ▴ 20

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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?

ADD REPLY • link 19 months ago by Jesse ▴ 740

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

ADD REPLY • link 19 months ago by Yuki _ISHIKAWA ▴ 20

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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.

ADD REPLY • link 19 months ago by Jesse ▴ 740

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

ADD REPLY • link 19 months ago by Yuki _ISHIKAWA ▴ 20

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