Question: Genomic Bam To Transcriptome Bam
gravatar for dfernan
6.2 years ago by
United States
dfernan660 wrote:


I was looking for a tool to convert a bam file in genomic coordinates to transcriptomic coordinates (using a GTF reference). Is there a fast way to do this for large bam files? Such tool would filter out reads that do not map to any transcript.

Let me know if you have any suggestions,


Daniel F.

bam samtools • 3.6k views
ADD COMMENTlink modified 4.2 years ago by ngsbioinformatics30 • written 6.2 years ago by dfernan660

You'll probably get the best answer by simply mapping your reads to the transcripts directly if having transcript-based BAM files is really your goal. If, instead, you want read counts for your genomic BAM files, that can be done with several tools. If the latter is what you want, then perhaps you can clarify your question.

ADD REPLYlink written 6.2 years ago by Sean Davis25k

Hi Sean, thanks. The problem is that if I map directly to the transcripts I loose the ability to build new transcripts, find splice junctions, etc. Also in many cases I am dealing with totalRNA experiments so mapping only to transcripts I loose many reads. Let us say I already mapped all my data and just want to transform coordinates, there is no way to do this? Maybe you are right and it does not make much sense that's why it does not exist...

ADD REPLYlink written 6.2 years ago by dfernan660
gravatar for Biomonika (Noolean)
6.2 years ago by
State College, PA, USA
Biomonika (Noolean)3.1k wrote:

I believe that you may use bedtools intersect:

ADD COMMENTlink modified 6.2 years ago • written 6.2 years ago by Biomonika (Noolean)3.1k
gravatar for ngsbioinformatics
4.2 years ago by
United States
ngsbioinformatics30 wrote:

I believe you want this tool sam-xlate from UBU:

It doesn't take a GTF, but rather a BED file in refFlat (I believe) format.

ADD COMMENTlink written 4.2 years ago by ngsbioinformatics30
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