How to convert genomic position to transcript position?

Question

[biolab]

Dear all,

I have a genome mapping bam file, which contains the start position of the mapped reads. I would like to convert the genomic position to transcript position, for example, gene A locates at chr1:200-400, read B starts at chr1: 300, then read B is at position 101 of transcript A. I am working on Arabidopsis that has GFF file. Is there any tools to do this job?

Thank you for any of your suggestions!

[biocyberman]

I haven't used it directly, but map2gtf tool from Tophat seems to do the job (may be in the reversed way: transcript to genomic). If it does not do what you want, guess you have to write yourself a biopython script or bioconductor R script: https://support.bioconductor.org/p/62326/

Answer 1

[fanli.gcb]

I've used a modified version of the htseq-count utility from HTSeq in the past for this: https://github.com/fanli-gcb/Core.RNAseq/blob/master/sam2pos.py

Note that this requires the HTSeq module be installed.