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-   -   Getting protein fasta from RNAseq BAM file (human) paying attention on repeats (http://seqanswers.com/forums/showthread.php?t=87138)

pauli.pauli 01-12-2019 02:13 AM

Getting protein fasta from RNAseq BAM file (human) paying attention on repeats
 
Hi everybody,

I have several RNAseq BAM files (mapped with BWA and GATK IndelRealigner) of cancer patients of which I should compare if there any copynumber in repeats appeared (whole transcriptome). I need to find a pipeline to find repeats in with our repeat detection software which needs FASTA and protein sequences as input.

Now I would like to have each patient's personal transcriptome as Fasta format which I could only feed to our software. What do I do now? For example, can I use Blastx, which compares directly to a reference proteome? Does this pay attention to the reading-frame? How do I get a Fasta output with each protein? In this pipeline, it is important to pay special attention to repeats that deviate from the reference.

Many thanks for your help!


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