From aligened sliced and filtered bam to single sequence in fasts format
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6.6 years ago
rus2dil ▴ 20
Hello, I have mapped 6 paired illumina raw reads against a reference genome and filtered by mapping quality and chromosome number 6. Then sliced using predefined coordinates of a gene region and merged the resulting bam files. Now I have a bam file of newly mapped genome only within the coordinates. So I want to get this sequence in fasta format. How do I do that in galaxy or using any other software?
Assembly galaxy • 1.9k views
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6.6 years ago

Hello,

I see the line-command options, but this can also be done very easily in Galaxy

  1. Login or create an account at http://usegalaxy.org
  2. Upload the BAM file. Use FTP (for data over 2G) http://wiki.galaxyproject.org/Support#Loading_data
  3. Use the tool "NGS: Picard -> SamToFastq"
  4. Then the tool "Convert Formats -> FASTQ to FASTA"
  5. Save the tools into Workflow for reuse quickly with the History option "Extract Workflow" http://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Extract

Hope this helps! Jen, Galaxy team

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