I need to get the introns coordinates (chr:strat-end and the strand) of the spliced reads wich are in SAM file.
I have no experience with this kind of format, so I plan to transform the SAMs files to BED12 files with this pipe line:
samtools view -bS -o file.bam file.sam && bamToBed -bed12 -i file.bam > file.bed12
And then, use galaxy or own python script (which I haven't wrote yet) to extract the introns from the spliced reads.
The problem with this method is weight of the files... it'll take some time to convert to BED12 and then extract the introns...
Do you know a more direct way to extract the introns coordinates from the SAMs files?