I have a bed file of some custom regions I have interest in, e.g.
chr1 1000 1015 my_region 0 + ...
I believe these regions may be translated, but are not necessarily annotated genes. So I would like to map some reads to these regions to confirm my suspicions.
The dataset GSE109313 has 1 Trillion reads from various human tissues.
Clicking on the run selector I can see the 37 SRR samples.
Using
prefetch
I downloaded these files.
Often reads are mapped to a GTF file, e.g. the human GTF file can be found on ensembl.
So now I have bed file or regions I would like to map to, the human GTF file, and the ~400Gb of SRR files.
Where do I go from here?
Map to the whole genome and then look at regions of your interest. Don't do it any other way, especially if original data is from entire genome.
so for clarity, use bowtie on file with hg38 and then what do you suggest to for looking at regions of my interest
You can use
mosdepth
(LINK) orbedtools coverage
(LINK) to look at your regions of interest.