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Search: Posts Made By: n00c
Forum: Bioinformatics 04-15-2011, 12:27 PM
Replies: 6
Views: 3,325
Posted By n00c
Sounds like you want to convert FASTA+QUAL to...

Sounds like you want to convert FASTA+QUAL to FASTQ. BioPython and BioPerl supposedly do this:

http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc218...
Forum: Bioinformatics 04-14-2011, 09:33 AM
Replies: 4
Views: 4,368
Posted By n00c
BWT-based mappers are theoretically fastest ones...

BWT-based mappers are theoretically fastest ones up until certain read length (don't remember exactly, but something like 400-1000 bp). There is a bunch of papers out there describing this.

Bowtie...
Forum: Bioinformatics 03-27-2011, 06:13 PM
Replies: 5
Views: 4,717
Posted By n00c
Actually Linux would be first choice because...

Actually Linux would be first choice because quite a few NGS bioinformatics tools are compiled with Linux in mind (to work on clusters, etc.).

A Mac is nice as a secondary workstation or as a...
Forum: Bioinformatics 03-27-2011, 05:58 PM
Replies: 2
Views: 2,373
Posted By n00c
It seems that most people prefer BWA over Bowtie...

It seems that most people prefer BWA over Bowtie for resequencing and targeted/capture sequencing like in your case, and Bowtie over BWA for RNA-seq (reason being that Bowtie does not handle indels...
Forum: Bioinformatics 03-18-2011, 08:58 PM
Replies: 8
Views: 11,811
Posted By n00c
There is also vcfutils vcf-isec: ...

There is also vcfutils vcf-isec:
http://vcftools.sourceforge.net/perl_module.html#vcf-isec
Forum: Bioinformatics 03-18-2011, 08:57 PM
Replies: 14
Views: 8,009
Posted By n00c
Have you tried running Picard with...

Have you tried running Picard with VALIDATION_STRINGENCY=LENIENT?
Forum: Bioinformatics 03-17-2011, 12:34 PM
Replies: 1
Views: 2,321
Posted By n00c
I don't know enough about mpileup, but in my case...

I don't know enough about mpileup, but in my case I found setting the RG tag useful because it allowed me to mark reads as belonging into two separate libraries for each of the individual genomes I...
Forum: Bioinformatics 03-17-2011, 12:20 PM
Replies: 11
Views: 3,687
Posted By n00c
SeqAn is a well-rounded and a well-designed...

SeqAn is a well-rounded and a well-designed library (there's even a book about it: http://www.amazon.com/Biological-Sequence-Analysis-Mathematical-Computational/dp/142007623X, which I found to be a...
Forum: Bioinformatics 03-15-2011, 08:28 AM
Replies: 3
Views: 1,927
Posted By n00c
RepeatMasker, most likely.

RepeatMasker, most likely.
Forum: Bioinformatics 03-14-2011, 07:54 PM
Replies: 5
Views: 3,841
Posted By n00c
The reason you are seeing reads with more...

The reason you are seeing reads with more mismatches than specified is because you have paired-end reads, and with paired-end read resolution usually you have a situation where one end maps to some...
Forum: Bioinformatics 03-13-2011, 03:44 PM
Replies: 4
Views: 3,938
Posted By n00c
I just created a small BAM file from the three...

I just created a small BAM file from the three lines you posted, and there was no segfault on executing "samtools view -h file.bam > out.sam," with out.sam being the same as input SAM. This seems to...
Forum: Bioinformatics 03-09-2011, 04:50 PM
Replies: 2
Views: 2,180
Posted By n00c
Mosaik supports IUPAC codes during alignment...

Mosaik supports IUPAC codes during alignment phase, but I don't know whether it uses them during the actual mapping.
http://bioinformatics.bc.edu/marthlab/Mosaik
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