How to align raw data to custom regions of the genome?
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
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?
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
Code:
prefetch
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?