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Forum: Bioinformatics 02-16-2016, 04:01 AM
Replies: 10
Views: 4,326
Posted By GenoMax
Disclaimers in the last post still apply :) ...

Disclaimers in the last post still apply :)

Step 1: Grab a listing of the Read1 files

$ ls -1r /Users/juanc/projectscx/reads/taxon*/clean/*READ1*.fastq.gz > taxon_read1_list

Step 2: Verify...
Forum: Bioinformatics 02-15-2016, 01:31 PM
Replies: 10
Views: 4,326
Posted By GenoMax
I am going to assume that you are in the...

I am going to assume that you are in the directory where you have the sai files. Since I don't have your files use the following at your own risk :-)

NOTE: How many of these sample directories are...
Forum: Bioinformatics 02-15-2016, 10:54 AM
Replies: 10
Views: 4,326
Posted By GenoMax
See this: https://www.biostars.org/p/98222/ ...

See this: https://www.biostars.org/p/98222/

You would need to change the actual command and parsing criteria based on your file names. If you post example file names we can help with the commands....
Forum: Bioinformatics 02-15-2016, 09:14 AM
Replies: 10
Views: 4,326
Posted By GenoMax
Are you asking for an example for @piet's comment...

Are you asking for an example for @piet's comment or for the actual loop?

For @piet's comment:

Replace /provide_path_to/ part with real or relative paths from your computer.

$ bwa sampe...
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