How to identify RNA-seq reads spanning given genomic range?
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2.6 years ago
agicict ▴ 180

I am working on RNA sequencing data from glioblastoma samples.

One of the most famous variant in glioblastoma is EGFR variant III.

EGFR variant iii is aberrant EGFR protein without exon 2-7 regions, which is not detectable from my whole-exome sequencing data and variant callers.

Therefore, I tried to locate RNA-seq reads spanning from exon 1 to exon 8 with pysam (python3).

I used fetch function and extracted reads starting from exon 1 region with following command line.

loaded_bam.fetch('chr7',55086794,55087058)

Now, I need to identify RNA reads whose end nucleotides are situated in exon8 ('chr7',55224226,55224352).

How to identify them?

RNA-Seq python pysam • 533 views
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2.6 years ago
ATpoint 54k

Get the annotation (GTF or GFF3) file for your genome version and then grep out your gene and then the respective exon, basically as in here A: how to get intronic and intergenic sequences based on gff file?. These coordinates you can use with your code snipped from above.

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