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Automating Map NGS to Reference (Read 396 times)
Dec 21st, 2017 at 6:43pm

Mike   Offline
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I'm currently producing SAM alignments from NGS data using the 'Map Reads to reference' tool.  All going fine but I still have hundreds to process and wondered if anyone knew any terminal coding to run in bulk or automate.  I also can't seem to get the workflow designer to do it. 
Here is my current workflow:
- Tools - NGS - Map reads to reference
- Select Bowtie
- Identify ref sequence (always the same)
- Import 8 NGS fastq
- Run
- Then I 'export assembly region' to SAM across a defined bp range (Always the same).


Any advice...?
Many thanks Smiley
 
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