Forum: Bioinformatics
12-23-2011, 12:45 PM
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Replies: 0
Views: 1,098
Looking to release software to the NGS community
Hi SEQanswers,
First, let me apologize if this is not the right avenue to make this request. I am the author of pBWA - a parallel implementation of a Burrows-Wheeler transform based short read...
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Forum: Bioinformatics
12-23-2011, 12:28 PM
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Replies: 7
Views: 4,073
Sometimes insert sizes receive extremely high...
Sometimes insert sizes receive extremely high estimates for certain datasets - you can use the -A parameter to disable isize estimating altogether and enforce your own, IIRC.
And I believe...
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Forum: Bioinformatics
09-16-2011, 04:54 AM
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Replies: 52
Views: 18,860
Given it's the same error message in the same...
Given it's the same error message in the same function, I'm going to say RAM again - sampe/samse require more RAM than aln, because sampe/samse require every processor to have the entire suffix array...
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Forum: Bioinformatics
09-15-2011, 03:12 PM
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Replies: 52
Views: 18,860
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Forum: Bioinformatics
09-15-2011, 03:11 PM
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Replies: 52
Views: 18,860
Actually, BWA only has multi-threaded...
Actually, BWA only has multi-threaded functionality for half of the process. sampe/samse is not multithreaded. Moreover, BWA's multithreading was inefficient when I initially released pBWA for...
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Forum: Bioinformatics
09-15-2011, 11:05 AM
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Replies: 52
Views: 18,860
It could possibly be a RAM issue... with MPI...
It could possibly be a RAM issue... with MPI applications each instance of the program is completely separate from another. Ie. where threaded applications share global variables, MPI applications...
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Forum: Bioinformatics
09-15-2011, 10:46 AM
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Replies: 52
Views: 18,860
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Forum: Bioinformatics
09-14-2011, 03:21 PM
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Replies: 52
Views: 18,860
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Forum: Bioinformatics
08-23-2011, 06:36 AM
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Replies: 52
Views: 18,860
Hi Sheng,
You need to figure out the alias...
Hi Sheng,
You need to figure out the alias to use to call the MPI compiler. On most clusters this will be "mpicc"... you'll have to contact your system administrator to figure out what this is,...
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Forum: Bioinformatics
08-23-2011, 04:22 AM
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Replies: 52
Views: 18,860
Hi sheng,
These requirements can be broken...
Hi sheng,
These requirements can be broken down as follows. pBWA is a _parallel_ implementation of BWA. This means that unless your computer system has multiple processors, this software will be...
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Forum: Bioinformatics
07-25-2011, 12:23 PM
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Replies: 6
Views: 4,047
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Forum: Bioinformatics
07-05-2011, 06:56 AM
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Replies: 52
Views: 18,860
Just to let everyone know, an alternate version...
Just to let everyone know, an alternate version of pBWA is now available (http://sourceforge.net/projects/pbwa) that cleans up the workflow a bit. The user is no longer required to enter the number...
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Forum: Bioinformatics
06-22-2011, 07:16 AM
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Replies: 5
Views: 2,196
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Forum: Bioinformatics
06-21-2011, 09:22 PM
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Replies: 5
Views: 2,196
Just write a shell script that calls your three...
Just write a shell script that calls your three commands in order... unless you are executing BWA on a server with a scheduler, in which case you can just submit all three commands independently with...
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Forum: Bioinformatics
06-21-2011, 05:24 AM
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Replies: 9
Views: 6,958
It says in the paper that BWA will find all...
It says in the paper that BWA will find all single-end alignments for each mate and sort them in ascending order of chromosomal coordinates. Then it uses an estimated insert size to determine which...
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Forum: Bioinformatics
06-16-2011, 08:34 PM
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Replies: 1
Views: 2,153
If you're getting core dumps, it means your...
If you're getting core dumps, it means your program run is crashing, likely due to an invalid memory access causing a segmentation fault.
Try analysing your core dumps with gdb if your system has...
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Forum: Bioinformatics
06-15-2011, 02:14 PM
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Replies: 1
Views: 2,629
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Forum: Bioinformatics
06-15-2011, 05:16 AM
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Replies: 3
Views: 6,032
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Forum: Bioinformatics
06-14-2011, 08:15 PM
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Replies: 1
Views: 1,510
Oh, wait, now it looks like the sequence and...
Oh, wait, now it looks like the sequence and reverse sequence (p->seq & p->rseq) in the code are actually identical unless they are SOLiD reads, in which case they are simply complements (but NOT...
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Forum: Bioinformatics
06-14-2011, 08:06 PM
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Replies: 1
Views: 1,510
BWA & Reverse Sequences
Hi all,
Just wanted to clear something up. When BWA reads the input sequences, it generates the reverse sequence for each read. Then, when searching for matches, it will check both the forward...
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Forum: Bioinformatics
06-14-2011, 02:48 PM
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Replies: 1
Views: 1,940
BWA determines the suffix array intervals for...
BWA determines the suffix array intervals for each read during the 'aln' stage. If you're allowing errors (bwa aln -n #oferrors), a read can have many suffix array intervals of varying lengths.
...
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Forum: Bioinformatics
06-01-2011, 12:09 PM
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Replies: 1
Views: 1,802
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Forum: Bioinformatics
05-27-2011, 11:56 AM
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Replies: 25
Views: 12,949
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Forum: Bioinformatics
05-27-2011, 11:41 AM
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Replies: 25
Views: 12,949
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Forum: Bioinformatics
05-27-2011, 11:22 AM
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Replies: 25
Views: 12,949
Yeah, it's a weird feature. Using the -a...
Yeah, it's a weird feature. Using the -a parameter, it should be clear that you want to override the program's estimating process, but for some reason the -a parameter becomes a fallback value.
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