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Old 04-04-2013, 08:12 AM   #1
vivienne_lovely
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Question 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.

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Old 04-26-2013, 12:01 AM   #2
SpreeFu
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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!
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Old 04-26-2013, 02:58 AM   #3
shi
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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.
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Old 04-26-2013, 06:31 AM   #4
SpreeFu
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Quote:
Originally Posted by shi View Post
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!
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Old 04-26-2013, 07:51 AM   #5
vivienne_lovely
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Quote:
Originally Posted by shi View Post
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
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Old 04-19-2016, 11:39 AM   #6
bvk
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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.
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