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Forum: Bioinformatics

06-11-2010, 08:51 AM

Replies: 0

Anyone using Roche's aligners?

Views: 1,207

Posted By bbimber

Anyone using Roche's aligners?

Is anyone using roche's reference guided aligner with 454 data? I see many posts about other aligners on this, but barely see mention of roche's tools. while roche's tools are free i think, roche...

Forum: Bioinformatics

06-11-2010, 08:49 AM

Replies: 2

Samtools pileup coverage issue

Views: 1,991

Posted By bbimber

there's a good perl API for samtools if you want...

there's a good perl API for samtools if you want to go that route. google Bio::DB::Samtools or something along those lines and you'll find it.

Forum: Bioinformatics

04-22-2010, 09:21 PM

Replies: 3

Mosaik: possible for MosaikText to create SAM or BAM, but not compress it?

Views: 2,278

Posted By bbimber

correction: the BAM file produced my mosaik can...

correction: the BAM file produced my mosaik can be used as is.

Forum: Bioinformatics

04-22-2010, 04:21 PM

Replies: 1

bwasw: get SAM output containing all hits per query?

Views: 1,701

Posted By bbimber

bwasw: get SAM output containing all hits per query?

when running bwasw (not bwa aln) is it possible to produce a SAM output containing all matches per read, not just one hit? i've seen a number of posts asking this question about bwa aln, but have...

Forum: Bioinformatics

04-22-2010, 04:08 PM

Replies: 3

Mosaik: possible for MosaikText to create SAM or BAM, but not compress it?

Views: 2,278

Posted By bbimber

Mosaik: possible for MosaikText to create SAM or BAM, but not compress it?

MosaikText can convert a mosaik output into either SAM or BAM files; however, it always produces a zipped output. Is there a way to make it produce one of these formats without gzipping it?

Forum: Bioinformatics

03-20-2010, 04:44 PM

Replies: 3

Questions about maniupating Sam format

Views: 4,543

Posted By bbimber

thanks for the reply. one more question: ...

thanks for the reply. one more question:

an example pileup output, might look like:

seq1 272 T 24 ,.$.....,,.,.,...,,,.,..^+. <<<+;<<<<<<<<<<<=<;<;7<&

If I wanted to use this data to...

Forum: Bioinformatics

03-20-2010, 10:44 AM

Replies: 0

generate CIGAR string from 2 sequences?

Views: 1,730

Posted By bbimber

generate CIGAR string from 2 sequences?

do pre-existing tools or scripts exist to generate a CIGAR string from two aligned sequence strings?

Forum: Bioinformatics

03-20-2010, 10:42 AM

Replies: 3

Questions about maniupating Sam format

Views: 4,543

Posted By bbimber

Questions about maniupating Sam format

We are building an analysis pipeline for 454 sequence based genotyping. We compare each 454 read against a reference cDNA library and want to ask which sequences the read aligns against, and how...

Forum: Bioinformatics

03-16-2010, 06:11 AM

Replies: 9

Quality trimmming / Mask low quality bases?

Views: 5,757

Posted By bbimber

if you are interested in illumina, look into...

if you are interested in illumina, look into fastx toolkit (link above). there's a command line tool to do it. they might also have a web interface for it, but i'm not 100% positive. the logic...

Forum: Bioinformatics

02-23-2010, 06:17 AM

Replies: 1

BLAT or BLAST: output SNPs between reference and query?

Views: 3,038

Posted By bbimber

BLAT or BLAST: output SNPs between reference and query?

When using either BLAT or BLAST, does anyone know of a tool or script that takes the output from the alignment and calculates the positions of difference between the reference and query?

For...

Forum: Bioinformatics

01-27-2010, 10:32 AM

Replies: 9

Quality trimmming / Mask low quality bases?

Views: 5,757

Posted By bbimber

ok, thanks for the reply. that's the impression...

ok, thanks for the reply. that's the impression I was getting from google.

in case anyone else reads this, i did come across this:

http://hannonlab.cshl.edu/fastx_toolkit/index.html

Forum: Bioinformatics

01-27-2010, 08:15 AM

Replies: 9

Quality trimmming / Mask low quality bases?

Views: 5,757

Posted By bbimber

Quality trimmming / Mask low quality bases?

Does anyone know of a command line utility that can accept either FASTA/QUAL or FASTQ files and mask any bases below a given quality score (ie. convert them to N)?

Does anyone have suggestions on...

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