How to align raw data to custom regions of the genome?

sumneuron · 03-24-2020, 04:19 AM

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

Code:

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?

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03-24-2020, 04:19 AM	#1
sumneuron Junior Member Location: Germany Join Date: Mar 2020 Posts: 1	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 Code: 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?