analyse bam file

Question

[priscilladraj]

Hi, I am really new to any bioinformatics analysis. So please, if you could answer me in the most simplest form I would trully appreciate it. I have two bam files (bam 1 and bam 2) that were generated when I aligned one fastq read file to two reference sequences (ref 1 ref2) fasta format. When I view my sorted bam file in IGV , I am unable to see how many reads were aligning to ref1 and ref2? I have a virtual ubuntu machine that I am using to anaylse the above data. Could someone help me out please. Thanks so very much. Pris

[husensofteng]

Generally speaking, most of these tasks can be accomplished with BEDTools and since you are new to Bioinformatics I suggest you read its documentation and get acquitted with its various tools.

Here to find the overlapping reads between bam1 and bam2 you could use intersect.

Also, to get stats on the contents of a BAM file you could use: samtools stats

Finally, before posting new questions it is always good to search the forum or even goole because usually it might be answered somewhere else

[wulj2]

strongly recommend samtools stats

[bas1993]

Besides Bedtools and samtools, I think Bamstats is also useful.

Answer 1

[priscilladraj]

Thanks I actually used samstat I was able to get the number aligned reads. I am new to Biostar too , so i didnt see this replies until today. Thanks :)

[wulj2]

what you choose can not be more right