Tag: UMItools
Can I use umi_tools to discard cell barcodes and extract the UMI while keeping the UMI in the read?
Can I use umi_tools to discard cell barcodes and extract the UMI while keeping the UMI in the read? 0 I have paired end reads where the read structure is as follows: >Read1 5′-6N-20CB-XXXXXXXXXX….XXXXGS-3′ The 6N corresponds to the UMI, the 20CB corresponds to 20 basepairs of cell barcode and…
Nextflow memory issues custom config -c
Nextflow memory issues custom config -c 1 Hi all, I am trying to run nextflow on my laptop nextflow run nf-core/rnaseq \ –input samplesheet.csv \ –genome mm10 \ -profile docker I am having issues with memory: Error executing process > ‘NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (KO_3)’ Caused by: Process requirement exceed available memory –…
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…
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…
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…
