Tag: UMItools

Track Clonotypes with TCR Sequence on standard Single Cell data (not scTCR-Seq)

Track Clonotypes with TCR Sequence on standard Single Cell data (not scTCR-Seq) 1 Hello, I used MIXCR on standard Single Cell data and found some common clonotypes among my multiple conditions. I would like to know if it would be possible to track clonotypes with the TCR Sequence ? If…

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BULK mRNA-seq with UMIs. Do I need to normalize by gene length?

Hi, I am analyzed some BULK mRNA-seq data that included UMIs during the sequencing. I don’t have much experience analyzing bulk RNA-seq, and it is my first time dealing with UMIs there. I have more experience in single-cell RNA-seq, and I thought that the concept of UMIs will translate directly…

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UMItools dedup deduplication taking too much time + RAM

I have some RNAseq data from miRNAs that I have processed with Bowtie2 (aligning to miRBase). Now, when doing the deduplication with umi_tools dedup I find that some of the files take a lot of time+RAM to finish (some files take around 3-4 minutes and 4-5GB of RAM and some…

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