Manipulation with coverage files/bedgraphs etc.

Question

[dominik.saburo]

Hi there!

I have a problem with my coverage files. My Miniseq gave me something like this:

Region,Coverage
ABCA1_Cds (49723720)_155448188.1,364
ABCA1_Cds (49723720)_155448189.1,406
ABCA1_Cds (49723721)_155448190.1,330
ABCA1_Cds (49723722)_155448191.1,92
ABCA1_Cds (49723722)_155448192.1,48
ABCA1_Cds (49723723)_155448193.1,444
ABCA1_Cds (49723723)_155448194.1,213
ABCA1_Cds (49723724)_155448195.1,298
ABCA1_Cds (49723724)_155448196.1,335
ABCA1_Cds (49723725)_155448197.1,205

It's an example of my coverage file from one of my patients. Can I make an alternative coverage file which will show me the number of exon instead of region coordinates?

I would like to have something like this:

"Gene name _ exon number_ read counts per region"

I use bedtools to make such bedgraphs but I can only make:

chr1    156106676   156106850   6059
chr1    55525249    55525436    2304
chr1    25870150    25870335    4
chr1    25883730    25883916    2004
chr1    25883610    25883786    2004
chr1    25880519    25880698    2684
chr1    25880383    25880571    2684
chr1    25881319    25881496    3400
chr1    25890254    25890444    6052
chr1    25890118    25890307    6052
chr1    25893431    25893612    3534
chr1    25893303    25893484    3534
chr1    25891626    25891807    758
chr1    25889097    25889276    3061
chr1    25889529    25889702    1479
chr1    55505603    55505783    2388

I use my manifest as a reference and this manifest has only columns with gene name, id, chromosome, coordinates etc.