How to count the reads mapping to different regions from tophat output

vivienne_lovely · 04-04-2013, 08:12 AM

Hi All.

I just mapped the RNA-Seqs by Tophat and got the output file accepted_hit.bam. I want to count the reads mapping to different regions such as exon,intron,exon-exon junction,exon-intron junction intergenic,rRNA and so on. I am really new in this field. Is there any software or custom script can do this? If you have a script can do this, would you please share it with me?Thank you very much.

Any reply will be appreciated.

Best

SpreeFu · 04-26-2013, 12:01 AM

Dear all, I also want to know how to count reads mapping to different regions of one gene. Could any one do me the favor? Thanks!

shi · 04-26-2013, 02:58 AM

The featureCounts function included in the bioconductor package Rsubread can count reads for you - http://bioconductor.org/packages/rel.../Rsubread.html .

It accepts both SAM and BAM format input files. By default, it assigns reads to NCBI RefSeq exons and/or genes. But you can provide your own annotation.

SpreeFu · 04-26-2013, 06:31 AM

Quote:

Originally Posted by shi

The featureCounts function included in the bioconductor package Rsubread can count reads for you - http://bioconductor.org/packages/rel.../Rsubread.html .

It accepts both SAM and BAM format input files. By default, it assigns reads to NCBI RefSeq exons and/or genes. But you can provide your own annotation.

Hi Shi, Thanks! I'm going to try it.
Have a nice weekend!

vivienne_lovely · 04-26-2013, 07:51 AM

Quote:

Originally Posted by shi

The featureCounts function included in the bioconductor package Rsubread can count reads for you - http://bioconductor.org/packages/rel.../Rsubread.html .

It accepts both SAM and BAM format input files. By default, it assigns reads to NCBI RefSeq exons and/or genes. But you can provide your own annotation.

Hi Shi,
Thank you for your help.

vivienne

bvk · 04-19-2016, 11:39 AM

Hi Shi,

how to do the same on linux? I want reads mapped to rRNA regions. how to do that? I have gtf and bam file.

In featureCounts manual it is given.

featureCounts -p -t exon -g gene_id -a hg19_RefSeq.gtf -o counts.txt accepted_hits.bam

This Summarize paired-end reads and count fragments (instead of reads).

Is this right one to count read pairs mapped to rRNA regions. Could you please help me.

Thank you

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04-04-2013, 08:12 AM	#1
vivienne_lovely Member Location: China Join Date: Oct 2011 Posts: 20	How to count the reads mapping to different regions from tophat output Hi All. I just mapped the RNA-Seqs by Tophat and got the output file accepted_hit.bam. I want to count the reads mapping to different regions such as exon,intron,exon-exon junction,exon-intron junction intergenic,rRNA and so on. I am really new in this field. Is there any software or custom script can do this? If you have a script can do this, would you please share it with me?Thank you very much. Any reply will be appreciated. Best

04-19-2016, 11:39 AM	#6
bvk Member Location: czech Join Date: May 2015 Posts: 65	Hi Shi, how to do the same on linux? I want reads mapped to rRNA regions. how to do that? I have gtf and bam file. In featureCounts manual it is given. featureCounts -p -t exon -g gene_id -a hg19_RefSeq.gtf -o counts.txt accepted_hits.bam This Summarize paired-end reads and count fragments (instead of reads). Is this right one to count read pairs mapped to rRNA regions. Could you please help me. Thank you Last edited by bvk; 04-20-2016 at 03:05 AM.

04-26-2013, 12:01 AM	#2
SpreeFu Member Location: Germany Join Date: Dec 2012 Posts: 24	Dear all, I also want to know how to count reads mapping to different regions of one gene. Could any one do me the favor? Thanks!

04-26-2013, 02:58 AM	#3
shi Wei Shi Location: Australia Join Date: Feb 2010 Posts: 235	The featureCounts function included in the bioconductor package Rsubread can count reads for you - http://bioconductor.org/packages/rel.../Rsubread.html . It accepts both SAM and BAM format input files. By default, it assigns reads to NCBI RefSeq exons and/or genes. But you can provide your own annotation.