Transcriptomic Coordinate Bam To Genomic Coordinate Bam

Question

[Ge]

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

/misc/ngseq/stow/tophat-2.0.4.Linux_x86_64/bin/bam2fastx --all --fastq ./tmp/left_kept_reads.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.Linux_x86_64/bin/fix_map_ordering --bowtie2-min-score 5 --max-mismatches 1 --sam-header ./tmp/genes.bwt.samheader.sam - - ./tmp/left_kept_reads.m2g_um.bam | /misc/ngseq/stow/tophat-2.0.4.Linux_x86_64/bin/map2gtf --sam-header ./tmp/genome_genome.bwt.samheader.sam /srv/GT/reference/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf - ./tmp/left_kept_reads.m2g.bam > ./logs/m2g_left_kept_reads.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!

[Bioch'Ti]

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.

[Ying W]

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

[Ying W]

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.

[tonatiuh.pena.centeno]

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.

TPC