Extracting only reads overlapping with a feature
Hi everyone,
I am working on a RNA-seq dataset generated with direct-RNA sequencing technology and the reads are rather bad. Out of 170K reads, only 90K are overlapping with a feature (according to HTseq-count). I was wondering if there was an easy way to extract only those reads as the other ones do not really interest me ?
Thanks in advance !
• 859 views
•
link
written
by
Florian BERNARD •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Does single-end short-read sequencing affect the mapping of mitochondrial and ribosomal RNA?
written by txema.heredia •
-
10x VDJ (TCR/BCR) BAM to fastq
written by predeus
-
Counting intronic reads in bulk RNA-seq
written by John Ma
-
Decontaminate RNASeq data from other cell types?
written by pennakiza
-
Low HTseq Feature Counts in Subset of RNA-seq Samples
written by kmyers2 •
-
How to identify long reads coming from ligated cDNAs before sequencing ?
written by Florian Bernard
-
Identifying covered genes from nanopore cDNA-seq reads
written by Florian Bernard
-
How to find alternative splicing isoforms in reads generated by nanopore sequencing experiment
written by Florian BERNARD •
-
look for sequences containing a specific motif
written by Florian BERNARD •
-
Which .gtf file should I use when aligning/counting total RNA?
written by Kristin Muench
Hello Florian BERNARD!
Questions similar to yours can already be found at:
We have closed your question to allow us to keep similar content in the same thread.
If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.
Cheers!