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Forum: Bioinformatics 03-08-2016, 03:08 PM
Replies: 0
Views: 522
Posted By juanc
This may seem like an obvious question. I have...

This may seem like an obvious question. I have two groups of DNA sequences (e.g. pop1 and pop2) for many loci and I want to know if any have fixed differences (e.g. pop1 has all A and pop2 has all G...
Forum: Bioinformatics 02-16-2016, 09:29 AM
Replies: 10
Views: 2,186
Posted By juanc
So I executed the commands and the output report...

So I executed the commands and the output report was telling me that it was looking for the .sai files in the "clean" directories. I decided to do steps 1-4 (below) in those directories and move over...
Forum: Bioinformatics 02-15-2016, 02:21 PM
Replies: 10
Views: 2,186
Posted By juanc
I updated my previous post.

I updated my previous post.
Forum: Bioinformatics 02-15-2016, 12:40 PM
Replies: 10
Views: 2,186
Posted By juanc
1. fastq naming: taxon86-READ1.fastq.gz +...

1. fastq naming: taxon86-READ1.fastq.gz + taxon86-READ2.fastq.gz and taxon24-READ1.fastq.gz + taxon24-READ2.fastq.gz, etc.

2. sai file naming: taxon86-read1.sai + taxon86-read2.sai and...
Forum: Bioinformatics 02-15-2016, 10:25 AM
Replies: 10
Views: 2,186
Posted By juanc
Sorry, I meant for the actual loop.

Sorry, I meant for the actual loop.
Forum: Bioinformatics 02-15-2016, 08:52 AM
Replies: 10
Views: 2,186
Posted By juanc
Thanks for the suggestion. Would it be possible...

Thanks for the suggestion. Would it be possible to provide a quick example?
Forum: Bioinformatics 02-14-2016, 09:30 AM
Replies: 10
Views: 2,186
Posted By juanc
bwa sampe on multiple samples at once

I'm looking to loop through many samples using the bwa sampe command.

Here is what the command looks like for one sample:

bwa sampe ref.fasta read1.sai read2.sai read1.fastq.gz read2.fastq.gz...
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