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Old 01-12-2019, 02:13 AM   #1
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Location: Switzerland

Join Date: Jan 2019
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Default 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!
pauli.pauli is offline   Reply With Quote

bam, fasta, rnaseq, translation

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