Question about tophat2 pipeline · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

Question about tophat2 pipeline

After using tophat I want to count genes with HTSeq and analyse in R with DEseq. But I have a question. I must input all pair-end fastq files of a experimental group once, or run a tophat for each pair-end fastq file?

tophat2

• 2,271 views • link

written 11.9 years ago by tiago211287

1 answer

If you have biological replicates, then you should run tophat for each replicate separately. This is because DEseq uses counts from each biological replicate to estimate the dispersion. I don't think HTseq is smart enough to handle library tags in the BAM file and produce counts for each library separately. Hope it makes sense to you.

• 0 views • link

written 11.9 years ago by Ashutosh Pandey

Yes you answered me. Thank you very much for your help.

• 1 views • link

written 11.9 years ago by tiago211287

Log in to answer this question.

More posts like this

HTseq-Count: Long processing time
written 4.3 years ago by Sarah •

Hi everyone, I'm processing BAM files using htseq-count and it takes very long time to produce the counts for each file. It is about pair-end …
HTSeq funny output
written 8.8 years ago by --panda-- •

I got some interesting output from the htseq-count. My alignment file have 9933765 reads My htseq.count have 60525122 none unique alignment I wonder if someone …
How to TMM after HTSeq-count?
written 10.6 years ago by tinmad •

I work on RNA sequencing at the moment. I've used tophat and cufflinks before, so now I'd like to do it in different way. My …
when using htseq-count, should I only count read-pairs whose two mates were both reported ?
written 10.7 years ago by Pei

Hi all: Working with pair-end RNA-seq data, I found that for some read-pairs, only one end/mate was reported by tophat-output sam file and then htseq-count. …
How is Tophat producing more alignments than input reads?
written 10.9 years ago by colin.kern

<p>I'm running Tophat on paired end reads which I've run through Trimmomatic, so the command is something like:</p> <p>tophat R1.paired.fastq.gz,R1.unpaired.fastq.gz,R2.unpaired.fastq.gz R2.paired.fastq.gz</p> <p>If I count the …
How the best way to verify the up and down regulated genes in a list of DE genes, generated from DE…
written 11.7 years ago by tiago211287

I have a table of DE genes from each experimental group. And I have a list of genes in each chromosome. I want to look …
Question about Volcano plot
written 11.9 years ago by tiago211287

In each volcano plot figure I must have only 1 Experimental group vs Control? I was thinking in a 3d volcano plot showing all 3 …
Aligning Paired-End Reads In Single-End Mode
written 13.5 years ago by GPR

<p>Hello,</p> <p>I have a question on how to align paired-end reads.</p> <p>In cases of very large fastq files, which make aligners like TopHat crash in …
How To Generate A Paired End File Suitable For Bwa
written 13.8 years ago by GPR

<p>A question about BWA and paired-end reads. In TopHat, one inputs the paired-end fastq file twice and the tool understands you have paired-end reads. I …
Rna-Seq Paired End Analysis
written 14.0 years ago by KS

<p>Hello everyone,</p> <p>I am trying to do RNAseq analysis on Paired end data Illumina. I have about 4 files for each sample (2 forward and …