From aligened sliced and filtered bam to single sequence in fasts format

Question

[rus2dil]

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?

[Ashutosh Pandey]

Convert Bam File To Fasta File

Answer 1

[Jennifer Hillman Jackson]

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