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

[vivienne_lovely]

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]

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]

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]

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]

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]

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