Hi Everybody,
I'm still quite new to the world of next-generation sequencing. I started to work with the Ion Torrent PGM several months ago.
I've got a question related to the analysis of the coverage depth of different nucleotides/dels/insertions on the base positions of my reads.
I normally use the bam and corresponding bai-files generated by the Torrent Suite Software and load them into the IGV-Genome Browser.
There, one can get information about single base position coverage by mouseover (see screenshot).
One can see the total base count, count of A/T/G/Cs (+ and - reads), and count of dels and insertions.
I would like to have this data in a table, to use it in an Excel spreadsheet.
Can anybody tell me, how I can extract this data from my bam/bai-files for a defined region of interest? I'd appreciate any hints.
The most preferred output would be a data table like this:
e.g.
chrom position total count count of:A+ A- T+ T- C+ C- G+ G- del+ del- ins+ ins-
chr13 33211005 50 20 21 2 3 0 0 0 0 2 0 1 1
I've searched the forums for related threads, but I only found some bioinformatic information that I couldn't understand. I'm just a biochemist, and I have no big skills in bioinformatics. E.g., I don't know about Linux OS and how to use software or commands there.
Any help is much appreciated.
Thank you very much in advance.
Greetings
Coru
I'm still quite new to the world of next-generation sequencing. I started to work with the Ion Torrent PGM several months ago.
I've got a question related to the analysis of the coverage depth of different nucleotides/dels/insertions on the base positions of my reads.
I normally use the bam and corresponding bai-files generated by the Torrent Suite Software and load them into the IGV-Genome Browser.
There, one can get information about single base position coverage by mouseover (see screenshot).
One can see the total base count, count of A/T/G/Cs (+ and - reads), and count of dels and insertions.
I would like to have this data in a table, to use it in an Excel spreadsheet.
Can anybody tell me, how I can extract this data from my bam/bai-files for a defined region of interest? I'd appreciate any hints.
The most preferred output would be a data table like this:
e.g.
chrom position total count count of:A+ A- T+ T- C+ C- G+ G- del+ del- ins+ ins-
chr13 33211005 50 20 21 2 3 0 0 0 0 2 0 1 1
I've searched the forums for related threads, but I only found some bioinformatic information that I couldn't understand. I'm just a biochemist, and I have no big skills in bioinformatics. E.g., I don't know about Linux OS and how to use software or commands there.
Any help is much appreciated.
Thank you very much in advance.
Greetings
Coru
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