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Search: Posts Made By: gaffa
Forum: Bioinformatics 05-21-2013, 12:33 PM
Replies: 9
Views: 1,692
Posted By gaffa
I think Stampy should also be mentioned here: ...

I think Stampy should also be mentioned here:

http://www.ncbi.nlm.nih.gov/pubmed/20980556
Forum: Bioinformatics 01-22-2013, 04:52 AM
Replies: 1
Views: 779
Posted By gaffa
Well, if you want to view and inspect the VCF...

Well, if you want to view and inspect the VCF file directly, UNIX text viewing tools such as the 'less' command are good. If you want you can make things easier on the eye by for example first...
Forum: Bioinformatics 11-12-2012, 05:04 AM
Replies: 6
Views: 4,488
Posted By gaffa
You should probably use much more than 1000 reads...

You should probably use much more than 1000 reads for FastQC - the program is pretty fast, I would use the whole fastq files if they are not enormous. What you can look at in the FastQC output is the...
Forum: Bioinformatics 11-12-2012, 04:45 AM
Replies: 6
Views: 4,488
Posted By gaffa
In the best case scenario, the people doing the...

In the best case scenario, the people doing the sequencing experiment will inform you about the sequence of the adapters used during the experiment. However this is not always the case. What you can...
Forum: De novo discovery 10-09-2012, 03:30 AM
Replies: 3
Views: 1,694
Posted By gaffa
One thing you can do to get a general overview is...

One thing you can do to get a general overview is to make pairwise dot-plots of the assemblies, using for example the mummerplot program from the MUMmer package (http://mummer.sourceforge.net/). The...
Forum: Bioinformatics 10-09-2012, 02:29 AM
Replies: 2
Views: 898
Posted By gaffa
I haven't tried it myself, but maybe this could...

I haven't tried it myself, but maybe this could be of interest: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0019816
Forum: Bioinformatics 10-03-2012, 07:58 AM
Replies: 4
Views: 1,292
Posted By gaffa
Generally you just need to keep the .bai file in...

Generally you just need to keep the .bai file in the same directory as the bam file and any program that needs it will read it automatically.
Forum: Bioinformatics 09-17-2012, 07:06 AM
Replies: 2
Views: 1,564
Posted By gaffa
BWA-SW performs local alignment and can output...

BWA-SW performs local alignment and can output several alignments per input read/sequence. So a given read or different parts of a read can be aligned to different places, which are all included in...
Forum: Bioinformatics 08-06-2012, 05:03 AM
Replies: 252
Views: 98,593
Posted By gaffa
Is there any easy way to find out for a given...

Is there any easy way to find out for a given SSPACE scaffold what are the names of the pre-SSPACE contigs/scaffolds that are included in it?
Forum: Bioinformatics 07-22-2012, 11:45 PM
Replies: 14
Views: 2,557
Posted By gaffa
You might try running a local realignment program...

You might try running a local realignment program such as SRMA.
Forum: Bioinformatics 07-16-2012, 09:30 AM
Replies: 2
Views: 1,165
Posted By gaffa
BWASW (part of the bwa program) works fine for...

BWASW (part of the bwa program) works fine for this task.
Forum: Bioinformatics 06-30-2012, 10:07 AM
Replies: 6
Views: 2,988
Posted By gaffa
luckylove problably means "Mauve":...

luckylove problably means "Mauve": http://gel.ahabs.wisc.edu/mauve/
Forum: Bioinformatics 06-17-2012, 04:36 AM
Replies: 1
Views: 1,037
Posted By gaffa
What you could do is just to run once with these...

What you could do is just to run once with these lengths, and then once with the second pair trimmed down to a length of 44 bp as well, and see how it affects the results.
Forum: Bioinformatics 05-31-2012, 02:59 AM
Replies: 2
Views: 1,059
Posted By gaffa
Right here: http://www.yeastgenome.org/

Right here: http://www.yeastgenome.org/
Forum: Bioinformatics 05-29-2012, 01:39 AM
Replies: 9
Views: 1,810
Posted By gaffa
Actually they are of equal length, it's just that...

Actually they are of equal length, it's just that the forum font is not monospaced.
Forum: Bioinformatics 05-28-2012, 02:46 AM
Replies: 2
Views: 833
Posted By gaffa
For starters you can have a look at the end of...

For starters you can have a look at the end of the SAM specification: samtools.sourceforge.net/SAM1.pdf
Forum: Genomic Resequencing 05-18-2012, 12:05 PM
Replies: 4
Views: 7,972
Posted By gaffa
Unless you want to do something really...

Unless you want to do something really sophisticated it's often easy to parse things out with simple unix one-liners (cut, grep, awk etc.) and format them into the Circos formats.
Forum: RNA Sequencing 05-18-2012, 06:54 AM
Replies: 2
Views: 2,342
Posted By gaffa
Do you have read group information specified in...

Do you have read group information specified in the two files?
Forum: Bioinformatics 05-16-2012, 07:11 AM
Replies: 2
Views: 778
Posted By gaffa
Maybe this could be of interest:...

Maybe this could be of interest: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0019816
Forum: Bioinformatics 05-04-2012, 02:51 PM
Replies: 2
Views: 1,545
Posted By gaffa
I think I have encountered this problem - if I...

I think I have encountered this problem - if I remember correctly I think the problem is that SMALT puts "unknown" as the value for the SO tag and that this value is not allowed by Picard. I think it...
Forum: Bioinformatics 04-26-2012, 05:34 AM
Replies: 6
Views: 2,087
Posted By gaffa
Maybe you could post the output here?

Maybe you could post the output here?
Forum: Bioinformatics 04-16-2012, 10:39 AM
Replies: 4
Views: 1,675
Posted By gaffa
The term "mappability" has emerged to refer to...

The term "mappability" has emerged to refer to this - using this as a search term is likely to yield results. There are a few tools that compute mappability measures, for example GEM:...
Forum: Bioinformatics 04-14-2012, 04:32 AM
Replies: 4
Views: 3,289
Posted By gaffa
Check out the 'bamleftalign' utility which comes...

Check out the 'bamleftalign' utility which comes with the FreeBayes SNP caller, it should do this.
Forum: Bioinformatics 03-20-2012, 06:31 AM
Replies: 252
Views: 98,593
Posted By gaffa
Ok, great! Thanks. On a slightly related...

Ok, great! Thanks.

On a slightly related note, how well do you think SSPACE would deal with scaffolding information from other sources than paired/mate-reads, such as e.g. physical/genetic linkage...
Forum: Bioinformatics 03-18-2012, 03:30 PM
Replies: 252
Views: 98,593
Posted By gaffa
Is it possible to run SSPACE on external read...

Is it possible to run SSPACE on external read mappings, i.e. can I perform the read mappings on my own and then have SSPACE do the scaffolding based on them?
Showing results 1 to 25 of 82

 


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