Samview from bam file aligned to cDNA reference
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5.6 years ago
bharata1803 ▴ 530

Hello,

So I have a bam file from alignment to cDNA reference from Ensembl Hg38. Suppose transcript ID is T1. The length of the transcript is 15000. I want to extract the reads that aligned to T1 at position between 200-400. I think this is possible for the ordinary bam file which is aligned to human genome reference. I remember just specify chr1:pos1-pos2. How can I extract reads that correspond to a particular transcript ID and base position.

RNA-Seq sam bam • 1.5k views
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if you know the position of T1 on the genome, the process is called "translation" ...

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