Question: RNA-seq analysis using R
0
gravatar for justinkablan225
3 months ago by
justinkablan2250 wrote:

Hello all,
I'm a student and a beginer with R tool for RNA-seq analysis.
I've some Fastq files that I want to (i) convert into BAM file using LIMMA package in R and (ii) make an alignment with genome reference using Toophat tool.

The probleme is that, after reading the LIMMA userguide, I didn't catch what scripts use for those preliminary analysis.

May you help me if possible.

Sincerly.

rnaseq limma convert R • 172 views
ADD COMMENTlink modified 3 months ago by Gordon Smyth36k • written 3 months ago by justinkablan2250

Please only tag relevant packages as this emails the package maintainer. I removed the DESeq2 tag.

ADD REPLYlink written 3 months ago by Michael Love22k
Answer: RNA-seq analysis using R
1
gravatar for Gordon Smyth
3 months ago by
Gordon Smyth36k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth36k wrote:

The Rsubread package maps reads to a reference genome (which is how you convert FASTQ files into BAM). See

https://www.biorxiv.org/content/early/2018/07/26/377762

or

http://bioinf.wehi.edu.au/RNAseqCaseStudy/

TopHat is obsolete now; even the TopHat authors themselves recommend that you use newer tools.

ADD COMMENTlink modified 3 months ago • written 3 months ago by Gordon Smyth36k
Answer: RNA-seq analysis using R
0
gravatar for James W. MacDonald
3 months ago by
United States
James W. MacDonald49k wrote:
  1. limma isn't designed to convert FASTQ files into BAM files. After reading (?) the limma User's Guide, I am mystified as to why you would think that it is intended for that purpose. Can you say why you think that?
  2. TopHat isn't a Bioconductor tool, and this is a forum to help people use Bioconductor tools only. You could post your question about TopHat on Biostars.org, or better yet just read the TopHat manual. You will get much farther by doing your own learning rather than simply trying to get others to write a tutorial for you.
ADD COMMENTlink written 3 months ago by James W. MacDonald49k

Hi

I done some mistakes in my message but now I begin to understand better more.

Thus, I'm a Bioconductor tool user.

Best regard

ADD REPLYlink written 3 months ago by justinkablan2250
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