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Forum: Bioinformatics 05-21-2018, 08:43 AM
Replies: 0
Views: 865
Posted By aunderwo
BWA-mem and BWA-aln reads with multiple mapping

I have read that for bwa-aln

samse bwa samse [-n maxOcc] <in.db.fasta> <in.sai> <in.fq> > <out.sam>
Generate alignments in the SAM format given single-end reads. Repetitive hits will be randomly...
Forum: Illumina/Solexa 05-03-2013, 10:30 AM
Replies: 6
Views: 3,319
Posted By aunderwo
Torque and Casava


Did you have any success with this. We're hoping to do the same.

Forum: Bioinformatics 11-05-2011, 03:43 AM
Replies: 2
Views: 3,203
Posted By aunderwo
It turns out that you can specify the input...

It turns out that you can specify the input either as mpileup2snp out.pileup options OR mpileup2snp options < out.pileup.

The problem was --strand-filter needs an option (1 for on, 0 for off)
Forum: Bioinformatics 11-04-2011, 09:50 AM
Replies: 2
Views: 3,203
Posted By aunderwo
Varscan and mpileup

Hi all

does anybody gave any experience in using mpileup and then using varscans new mpileup2snp function to call SNPs?

I have generated 2 bam files and then used samtols mpileup to produce a...
Forum: Bioinformatics 09-23-2010, 07:01 AM
Replies: 8
Views: 3,149
Posted By aunderwo
I'd be happy to test

I am a bioinfomatician but have many users who would like to try software with an intuitive UI. Tried to pm you but this seemed to be disabled.

Please get in touch if looking for a beta tester
Forum: Introductions 09-23-2010, 06:59 AM
Replies: 1
Views: 1,040
Posted By aunderwo
Hello from HPA

Hi all

I work at the Health Protection Agency ( We are doing extensive work looking at variation n bacterial pathogens using Illumina and 454 data. Look forward to...
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