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Forum: Bioinformatics 02-20-2012, 03:54 PM
Replies: 5
Views: 3,287
Posted By attilav
Apparently the problem was some of the files...

Apparently the problem was some of the files getting corrupted during downloading. Sorry to have wasted your time with this... Guess I have learned a lesson to always check the MD5 sums when...
Forum: Bioinformatics 02-15-2012, 02:46 PM
Replies: 5
Views: 3,287
Posted By attilav
I made the genome index with bwa 0.6.1. I have...

I made the genome index with bwa 0.6.1.
I have 2GB RAM on this computer, which is not optimal, but the segfaults only happen, if there is a weird pairing before.
Its consistent.

I will align the...
Forum: Bioinformatics 02-15-2012, 03:55 AM
Replies: 5
Views: 3,287
Posted By attilav
BWA 0.6.1 fail to insert infer isize: weird pairing + Segmentation Fault

Hi all!

Using the command: bwa sampe refseq.fasta seq_1.aln.sai seq_2.aln.sai seq_1.fastq.gz seq_2.fastq.gz > output.sam , sometimes I get the error that you can see in the title. It looks like...
Forum: Bioinformatics 12-21-2011, 11:32 AM
Replies: 3
Views: 2,699
Posted By attilav
weird BWA SAM (samse) output

Hi all!

I've done an alignment job using BWA, and as a result, I've got myself an SAM file.
I read through the SAM format specification on samtools.sourceforge.net, I also checked out the example...
Forum: Bioinformatics 12-02-2011, 01:15 AM
Replies: 12
Views: 15,003
Posted By attilav
Changed the line in the makefile, and the make...

Changed the line in the makefile, and the make went through without an error!
Thank you!
Forum: Bioinformatics 12-01-2011, 01:18 PM
Replies: 12
Views: 15,003
Posted By attilav
installing Burrows-Wheeler Aligner (BWA) on windows

Hi all!

Can someone tell me, if it is possible to use BWA in windows, and if it is, then how can I install it?
I was told, that I should install a program called Cygwin, and use it to build BWA...
Forum: General 08-18-2011, 05:07 AM
Replies: 2
Views: 1,877
Posted By attilav
human genome short read data for "Do it yourself genetic testing"

Hi all!

I would really like to try a certain program (http://www.cbcb.umd.edu/software/BRCA-diagnostic/), because in some ways it's similar to a project I'm working on. My problem is, that I just...
Showing results 1 to 7 of 7

 


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