Is HTseq result based on uniquely mapped reads?

Dear all,

I heard from one of my colleague that HTseq result is based on uniquely mapped reads. Is that true? I think this point needs to be clarified, because HTseq-edgeR has been widely used for gene expression quantification. I appreciate any of your comments. THANKS!

htseq

• 4,108 views • link

updated 4.0 years ago by Ram

• written 10.7 years ago by biolab

1 answer

See the second question in the "FAQ" section for the htseq-count documentation.

• 0 views • link

updated 6.7 years ago by Ram

• written 10.7 years ago by Matt Shirley

Hi, Matt, the answer is very helpful!

• 0 views • link

written 10.7 years ago by biolab

Update 20th September 2018:

Now moved here for anybody else arriving here:

https://htseq.readthedocs.io/en/master/count.html

• 1 views • link

written 7.9 years ago by Kevin Blighe

More posts like this

Dealing with multiple-mapped reads in sRNA-seq
written 6.5 years ago by joaquinj12 •

I am trying to analyse small RNA-seq data with HtSeq, however, I have read that it is not appropriate enough as it just takes into …
What type of GTF file should I use for miRNAseq analysis?
written 7.2 years ago by silas008

Helllo, people! I am using edgeR to analise my small RNAseq data. I got a miRNA GTF file from UCSC site and used htseq to …
Removing shorter reads in PE mapping
written 9.3 years ago by biolab

Dear all, I have pair-end (PE) sequencing data (R1.fq and R2.fq). First, I removed the adapters, which resulted in unequal sequence length for some PE …
How to identify the loci producing differential small RNAs between two samples?
written 10.2 years ago by biolab

Hi, everyone, I have small RNA-seq data avaliable for two samples (wt and mutant), each of which have three replicates. I mapped the small RNAs …
Why some lines of BAM file do not contain NH tag
written 10.8 years ago by biolab

Hi, everyone, I want to get uniquely mapped reads, so need to select the NH (number of hits) tag value that is equal to 1. …
How to get unique mapped reads?
written 11.1 years ago by biolab

Dear all, Previously I thought when the `-g/--max-multihits` option in tophat was set to 1, then I acquired the unique mapped reads. However, after careful …
Tophat --max-multihits option
written 11.3 years ago by biolab

Dear all I have a simple question: Tophat2 has `--max-multihits` option. If I set it to one, does it mean that each read is mapped …
Cufflinks Question: how to find assembled parts differing from annotated parts?
written 11.4 years ago by biolab

Dear all I am new using tophat2 and cufflinks. To my knowledge, one function of cufflinks is to assemble mapped reads into longer parts based …
counting reads over repeats
written 11.9 years ago by R •

<p>To identify the expression levels of repeats in my RNA-Seq samples, I'm trying to count reads over repeats. The RNA-seq data (strand specific, dUTP ...) …
Protocol For Antisense Rna Analysis From Strand Specific Rna-Seq
written 12.5 years ago by liupfskygre

<p>Dear all</p> <p>I am working on 12 samples of strand specific bacterial RNA-seq data(4 reps for 3 treatment). I have finished the DE analysis by …