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Forum: Bioinformatics 12-05-2012, 07:32 AM
Replies: 12
Views: 3,221
Posted By Stina
Thank you so much for trying to help me. ...

Thank you so much for trying to help me.

The problem was that I was using bwa version 6.2, which obviously doesnt work properly on a mac, see http://seqanswers.com/forums/showthread.php?t=24133 ...
Forum: Bioinformatics 12-03-2012, 11:37 AM
Replies: 12
Views: 3,221
Posted By Stina
Hmm.. there is obviously something wrong with my...

Hmm.. there is obviously something wrong with my whole-genome fasta file..

1, when INDEX, give "-a bwtsw". (EDIT: no need to try this)
I tried anyway, and as you said it did not work.

2, just...
Forum: Bioinformatics 12-01-2012, 01:53 AM
Replies: 12
Views: 3,221
Posted By Stina
So I cut 1 million rows from my fastq file and...

So I cut 1 million rows from my fastq file and ran:

1) bwa aln ...fastq, which generated a 1 MB .sai file (one for each direction).

2) bwa sampe, which generates a 131.6 MB .sam file

bwa...
Forum: Bioinformatics 11-30-2012, 09:04 AM
Replies: 12
Views: 3,221
Posted By Stina
1) Run info (one of the two reads): multifasta...

1) Run info (one of the two reads): multifasta file generated from files from ensemble as ref genome sequence (60 MB output .sai file)

bwa aln refGen3.fasta...
Forum: Bioinformatics 11-30-2012, 12:38 AM
Replies: 12
Views: 3,221
Posted By Stina
Hi, Thank you so much for trying to help me....

Hi,

Thank you so much for trying to help me.

1) I run Mac OS X 64-bit and bwa is compiled in 64-bit

2) Indexing of my fasta file (bwa index my.fasta) takes about 50 min.

3) Output from...
Forum: Bioinformatics 11-29-2012, 03:25 AM
Replies: 12
Views: 3,221
Posted By Stina
too small output .sai file created by bwa aln? ..leads to bwa sampe hanging?

I have sequenced a 6MB region of a single chromosome of the dog genome (targeted capture).

At first I used a fasta file from GenBank of the particular chromosome as a reference sequence to map my...
Forum: Bioinformatics 11-28-2012, 11:50 PM
Replies: 3
Views: 1,162
Posted By Stina
Thanks for the advice!

Thanks for the advice!
Forum: Bioinformatics 11-28-2012, 12:23 AM
Replies: 3
Views: 1,162
Posted By Stina
Which .fa files should I include when creating a ref. genome of a non-human species?

I intend to analyse HTS resequencing data from a capture experiment in dogs and I am trying to create a reference genome to use for the analysis. I want to use the FASTA files at ensemble. The FASTA...
Forum: Sample Prep / Library Generation 02-29-2012, 05:01 AM
Replies: 0
Views: 1,386
Posted By Stina
COT Human DNA - used for dog samples?

I am planning a resequencing experiment targeting a region of the dog genome by using custom made probes from NimbleGen (EZ and array) but I am not sure whether I should use Cot-dna or not.
Does...
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