Question: Transcriptomic Coordinate Bam To Genomic Coordinate Bam
gravatar for Ge
6.7 years ago by
Ge80 wrote:

Hi, I want to ask how to convert the transcriptomic coordinate bam file to genomic coordinate bam. I mapped the reads to the transcriptome with bowtie2.

One possibe solution I found is that using tophat's map2gtf. In tophat's run.log

/misc/ngseq/stow/tophat-2.0.4.Linuxx8664/bin/bam2fastx --all --fastq ./tmp/leftkeptreads.bam|/usr/local/ngseq/bin/bowtie2-align -q -k 60 -D 15 -R 2 -N 0 -L 20 -i S,1,1.25 --gbar 4 --mp 6,2 --np 1 --rdg 5,3 --rfg 5,3 --score-min L,-0.6,-0.6 -p 8 --sam-no-hd -x ./tmp/genes -|/misc/ngseq/stow/tophat-2.0.4.Linuxx8664/bin/fixmapordering --bowtie2-min-score 5 --max-mismatches 1 --sam-header ./tmp/genes.bwt.samheader.sam - - ./tmp/leftkeptreads.m2gum.bam | /misc/ngseq/stow/tophat-2.0.4.Linuxx8664/bin/map2gtf --sam-header ./tmp/genomegenome.bwt.samheader.sam /srv/GT/reference/Musmusculus/UCSC/mm10/Annotation/Genes/genes.gtf - ./tmp/leftkeptreads.m2g.bam > ./logs/m2gleftkeptreads.out

However, I have no idea about how the --sam-header file was generated. I did not find any clue from the logs of tophat.

Anybody can help? Thanks!

bam convert genomics • 2.6k views
ADD COMMENTlink modified 6.7 years ago • written 6.7 years ago by Ge80

Hi, I have a very similar question. I've mapped reads on mRNA (CDS) and detect variants (SNPs). I would like to obtain the genomic coordinates of the discovered SNPs onto my reference genome. IS there any tools able to perform this task? Best, C.

ADD REPLYlink written 6.7 years ago by Bioch'Ti1000

It would be best if you opened up a new question and give more details such as what you mapped to.

ADD REPLYlink written 6.7 years ago by Ying W3.9k

I am guessing it is not possible for you to just remap it? (take your transcriptomic bam and run it through bowtie with reference as human genome instead of transcriptome). I am not quite sure what to make of the log output, the only thing I can think of is if you know where all the parts of your transcriptomic reference overlap with human reference then you can shft all the coordinates in a liftOver kinda way but not sure if liftOver would like references to be that different.

ADD REPLYlink written 6.7 years ago by Ying W3.9k

I wonder if you managed to run map2gtf, because I need to do the same as you, i.e. modify a bam file so that it contains genome coordinates instead of transcriptome coordinates.


ADD REPLYlink written 6.2 years ago by tonatiuh.pena.centeno0
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