Question: Using STAR aligner output for Htseq-count and Cufflinks
0
gravatar for candida.vaz
23 months ago by
Singapore
candida.vaz0 wrote:

Dear All,

I am using STAR aligner for mapping my paired end reads using the following parameters:

/cluster/apps/x86_64/packages/STAR_2.5/bin/STAR --runThreadN 4 --genomeDir /home/candidav/STAR-Gallus-gallus-nv5/Gallus-gallus-genome-dir-nv5 --readFilesIn /home/candidav/S1/RCI001-forward_paired.fastq /home/candidav/S1/RCI001-reverse_paired.fastq --outFilterType BySJout --outFilterIntronMotifs RemoveNoncanonical --outSAMtype BAM Unsorted SortedByCoordinate --outFileNamePrefix /home/candidav/Biomin-S1-RCI001-star-out/RCI001

Question1: Is this fine? or do I need to mention any other parameter?

Question2: I get these two output bam files, can I use them for the following downstream quantification tools?

  • RCI001-Aligned.sortedByCoord.out.bam : For Cufflinks

  • RCI001-Aligned.out.bam : For Htseq

Thanks in advance!

rna-seq • 2.3k views
ADD COMMENTlink modified 23 months ago by Devon Ryan89k • written 23 months ago by candida.vaz0
3
gravatar for Devon Ryan
23 months ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k wrote:
  1. That's a perfectly acceptable command.
  2. You don't need the file for htseq-count (featureCounts is much faster), you can use the same file as cufflinks.

As an aside, don't use cufflinks, use stringTie instead.

ADD COMMENTlink written 23 months ago by Devon Ryan89k

Hello Devon, Thanks for your answer! I was wondering what is feature count? I am using Htseq-count. http://www-huber.embl.de/HTSeq/doc/count.html

While running STAR --outSAMtype BAM Unsorted SortedByCoordinate we get two BAM files

STAR manual recommends to use the output Unsorted bam file for HTseq. My collaborators want me to use cufflinks, so can I use the SortedByCoordinate BAM file for quantification by cufflinks?

I have to learn how to use stringTie --thanks for recommending it.

Regards, Candida

ADD REPLYlink written 23 months ago by candida.vaz0
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