issue in gatc_counting.R

[ateissan]

Hello,

Could you please give the head of your gff file that you are using for gatc_counting.R? I am counting only half of the reads (only plus strand). Maybe my gff file is not well annotated.

Thanks Aurélie

[vhfsantos]

Hi Aurélie

Here it is:

##gff-version 1
##source-version rtracklayer 1.60.0
##date 2023-10-19
chr1    rtracklayer     sequence_feature        1       11163   .       .       .       chr1
chr1    rtracklayer     sequence_feature        11160   12414   .       .       .       chr1
chr1    rtracklayer     sequence_feature        12411   12464   .       .       .       chr1
chr1    rtracklayer     sequence_feature        12461   12689   .       .       .       chr1
chr1    rtracklayer     sequence_feature        12686   12832   .       .       .       chr1
chr1    rtracklayer     sequence_feature        12829   13318   .       .       .       chr1
chr1    rtracklayer     sequence_feature        13315   13423   .       .       .       chr1

We scan the whole genome (hg38) for GATC fragments and store the result as a GFF.

This file can be downloaded here.

Hope it helps.

Best, Vinícius