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Old 03-24-2020, 03:19 AM   #1
sumneuron
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Location: Germany

Join Date: Mar 2020
Posts: 1
Question 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?
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gtf annotation file, how-to, howto, mapping reads, next-gen sequencing

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