Extracting internal reads from SmartSeq3 data using zUMIs
Hi,
I am using the zUMIs pipeline to analyze SmartSeq3 data. I am looking for a way to extract the internal reads and map them separately from the UMI reads to get their genomic distribution across regions (introns, exons etc). How can I do this either using zUMIs or other tools? I am thinking a pattern search of 11bp tag present in the UMI containing read might be helpful here. Any suggestions are highly appreciated.
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Using UMI-tools on Smart-seq3 RNA-Seq data
written by Agastya •
-
Which zUMIs output to use for differential gene expression?
written by firestar
-
Different number of introns, exons, transcripts across RNA-Seq samples
written by lakshmi9c •
-
many intronic reads and no features counts in 3' RNA-seq sequencing
written by concetta •
-
Downsampling UMI reads
written by Bedirhan •
-
Demultiplexing and deduplicating using barcodes and UMIs in the "mate" read
written by lech.kaczmarczyk •
-
Profiling taxonomic distribution of genes in human gut microbiome
written by dazhudou1122
-
Analysis Pipelines for MBD-Seq Data
written by pm2012
-
How to analyze ChIP-Seq data to determine whether peaks are found on Exons, Introns, or Exon-Intron…
written by System
-
Higher Coverage In Introns Than Exons?
written by Rubal7
