Question: counting the reads mapped to specific coordinate in the genome
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gravatar for alirezamomeni707
24 months ago by
alirezamomeni7070 wrote:

I have RNA-seq data and aligned them to the genome, so I also have bam files. I also have the sequence of tRNA genes in the genome and corresponding coordinates. so, the question is that how can I count the number of reads that map to each coordinate separately in the genome. in other word, I want to count the number of reads that map to each tRNA variants. do you guys know how to do that?

rna-seq genome • 857 views
ADD COMMENTlink modified 24 months ago • written 24 months ago by alirezamomeni7070

did you look for an answer ? A simple google returns the answer.

ADD REPLYlink written 24 months ago by Pierre Lindenbaum119k

if you mean to use for instance HTseq_count, I have tried to use it but it needs GTF file which has information for all genes. if you get it from gencode or other websites, the information for the tRNA variants are not included. if I get the specific GTF file from the website relate to the the gene names and structure are different from what is mentioned in the GTF from gencode, HTseq count does not work. that is why I asked this question.

ADD REPLYlink written 24 months ago by alirezamomeni7070

Then make your own GTF file using the information you have (chromosome names, tRNA coordinates).

ADD REPLYlink modified 24 months ago • written 24 months ago by genomax66k

You can likely use your tRNA annotations (if GFF format) directly with several tools, otherwise convert to BED format which you should be able to use as intervals. Counting the reads can be done with several tools

ADD REPLYlink modified 24 months ago • written 24 months ago by Jon330
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