Extracting alignment coordinates from SAM file

Question

[dasakan]

Hi, I have a SAM alignment file. Alignment was done using BWA MEM between reference genome (in scaffolds, not a finished genome) and assembled transcripts (as contigs). I am interested to extract the genome coordinates of each contig/split contigs (as these are transcripts, so while aligning to the genomic sequence, may be aligned to different regions as split sequence due to exon/intron boundaries). Your suggestion will be highly appreciated:)

Thank you

[Pierre Lindenbaum]

contig,split,transcripts... I don't understand, please provide an example.

[dasakan]

Hi,

The meaning goes like this:

Contig: assembled sequences of RNA-seq reads, where each read is considered as transcript. As these sequences were generated from RNA sequences, so there will not be intronic sequences. Hence, if we align a contig sequence (mRNA/DNA) to genomic sequence, it may align to different parts of the genome to corresponding exons, which I mean different fragments of same contig sequence as 'split'. (N.B. I have on hand only the assembled contig sequence, without the RNA-seq reads).