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Forum: Bioinformatics 03-28-2012, 03:14 PM
Replies: 0
Views: 1,496
Posted By rcorbett
Question A can of Worms - Which all purpose aligner to replace BWA 0.5.7 for Illumina data?

Hi all,

Currently in our pipeline we are using BWA 0.5.7 in at least a part of all types of illumina data analysis.

By all types of data, I mean everything that comes off the sequencer. ...
Forum: Ion Torrent 02-17-2012, 07:29 AM
Replies: 15
Views: 14,356
Posted By rcorbett
Ion Torrent data quality impressions?

Hi.
We have an Ion Torrent PGM where we have sequenced a number of genomes. Looking at the TMAP alignments we definitely see sequencing errors of the indel variety around homopolymer regions in...
Forum: Bioinformatics 11-23-2011, 10:06 AM
Replies: 0
Views: 1,303
Posted By rcorbett
tophat max number of junctions per read?

Hi,
I can't seem to find any info that will inform me if there is a maximum number of junctions alignable by a read in tophat. Does anyone know if a single read can span 2 junctions when...
Forum: Bioinformatics 11-07-2011, 09:30 AM
Replies: 6
Views: 3,539
Posted By rcorbett
Hi Carlos, I did manage to reconstruct the...

Hi Carlos,
I did manage to reconstruct the files for mm9. It just required some reverse engineering.

I just downloaded the
ensGene.txt
refGene.txt
knownGene.txt
from UCSC then made...
Forum: Bioinformatics 09-23-2011, 08:35 AM
Replies: 6
Views: 3,539
Posted By rcorbett
tophat-fusion on mouse

Hi,
I see that tophat-fusion-post uses these files (included in the distribution):
ensGene.txt
ensGtp.txt
mcl
refGene_sorted.txt

But I'm not sure how to duplicate them for MM9. Can anyone...
Forum: Bioinformatics 08-11-2011, 09:48 AM
Replies: 0
Views: 1,512
Posted By rcorbett
which snp calling routine for tophat?

Hi All,
For our alignment based wtss pipeline we have been using bwa for alignment and SNVMix to identify snps.

We're checking out the new versions of tophat to see if they will be good...
Forum: Bioinformatics 06-29-2011, 01:16 PM
Replies: 20
Views: 9,557
Posted By rcorbett
Thanks everyone. The samples I usually look at...

Thanks everyone.
The samples I usually look at are tumour normal pairs of exome data. The best results I have gotten are achieved by filtering reads that align outside baits. This as mentioned...
Forum: Bioinformatics 06-29-2011, 07:48 AM
Replies: 20
Views: 9,557
Posted By rcorbett
Thanks for the helpful responses. I'm a...

Thanks for the helpful responses. I'm a little surprised that there aren't any tools that aren't tailored for exome CNV. However, I haven't been able to find anything via google, etc.

Anyone...
Forum: Bioinformatics 06-28-2011, 03:25 PM
Replies: 20
Views: 9,557
Posted By rcorbett
exome copy number and LOH

Hi folks,
Can anyone recommend a good tool for exome copy number analysis on Illumina data?

Ideally, but not necessarily, it would be a tool that includes GC correction.

We have an in-house...
Forum: Bioinformatics 05-13-2011, 09:19 AM
Replies: 3
Views: 2,696
Posted By rcorbett
CNV analysis on Illumina / Solid genomes

Hi all,

I had a look at the wiki and I see there are many tools available for getting copy number changes from read alignments. I am wondering if there is a particular accepted tool that comes...
Forum: Bioinformatics 02-17-2011, 07:04 AM
Replies: 5
Views: 3,568
Posted By rcorbett
Thanks for your input, Specifcially I've been...

Thanks for your input,
Specifcially I've been asked this by our group who are responsible for illumina sequencing.

They have cited the trade-off between tight distribution and yield, which...
Forum: Bioinformatics 02-16-2011, 07:27 AM
Replies: 5
Views: 3,568
Posted By rcorbett
"ideal" insert size

Has anyone discovered a study or formal recommendation of some sort that gives reason for chosing one ideal insert size for paried-end sequencing on human samples? I have been asked this by our...
Forum: Bioinformatics 09-16-2010, 09:47 AM
Replies: 2
Views: 3,410
Posted By rcorbett
picard markduplicates on huge files

Hey folks,
I'm trying to run markduplicates on some massive files (merged Solid bams), and often 100Gigs of RAM doesn't get the job done.

Does anyone have a good suggestion for a workaround. ...
Forum: Bioinformatics 06-30-2010, 10:47 AM
Replies: 11
Views: 7,012
Posted By rcorbett
If anyone is interested, Cole is working on a new...

If anyone is interested, Cole is working on a new version (0.8.3), that will improve these results.
Forum: Bioinformatics 06-25-2010, 12:52 PM
Replies: 11
Views: 7,012
Posted By rcorbett
I'm pretty jealous of your nice results! I have...

I'm pretty jealous of your nice results! I have played with cufflinks quite a bit and haven't seen a decent transcript such as that in all of my data.

Is it possible I am not seeing such good...
Forum: Bioinformatics 06-25-2010, 07:04 AM
Replies: 11
Views: 7,012
Posted By rcorbett
Hi thinkRNA, To run cufflinks, I used...

Hi thinkRNA,

To run cufflinks, I used entirely default parameters. I used the pre-compiled 0.8.2 beta version for 64bit linux. I didn't provide a gtf of reference exons because I wanted to...
Forum: Bioinformatics 06-23-2010, 08:06 AM
Replies: 11
Views: 7,012
Posted By rcorbett
Question cufflinks funny output, scripture comparison

Hi all,

I have 50bp paired illumina reads which I have aligned with tophat (default parameters).
The alignments look reasonable in IGV, or UCSC browser.

I have run scripture on the tophat...
Forum: Bioinformatics 05-05-2010, 01:13 PM
Replies: 35
Views: 19,340
Posted By rcorbett
I tried a workaround of changing all the "."...

I tried a workaround of changing all the "." characters in the sequence to "N" with awk:

awk '{if ( (NR-2)%4==0) {gsub(/\./,"N",$0); print $0} else { print $0}}'

Which gets me through...
Forum: Bioinformatics 05-05-2010, 12:36 PM
Replies: 35
Views: 19,340
Posted By rcorbett
I am getting the same error: This is with...

I am getting the same error:
This is with version tophat-1.0.13. Has anyone coded a fix for this?

@2065
AGGCCGCTCCGGGCGCTGGACGTTGGGCTCCTGGCGAACCTCTCGGCGCTGGAGACTGGATATAACACAAC...
Forum: Bioinformatics 04-19-2010, 07:01 AM
Replies: 2
Views: 3,409
Posted By rcorbett
For anyone who is following this. I re-ran this...

For anyone who is following this.
I re-ran this lane with bwa 0.5.5 and didn't have any problems.
Forum: Bioinformatics 04-16-2010, 06:59 AM
Replies: 2
Views: 3,409
Posted By rcorbett
bwa sampe 0.5.7 error?

Hi all,

I have paired genomic data (75bp) that I have "aln"-ed and am attempting to "sampe"

Everthing seems to get off to a decent start, getting through a few chunks of the file before...
Forum: Bioinformatics 02-10-2010, 10:12 AM
Replies: 2
Views: 2,625
Posted By rcorbett
Hmm. The editor ate the example. I'll use '#'...

Hmm. The editor ate the example.
I'll use '#' to mark spaces:

r1: ###GAG###
r2: ###GGG###
r3: ##AGA####
rf: AAAGGGTTTT
Forum: Bioinformatics 02-10-2010, 10:09 AM
Replies: 2
Views: 2,625
Posted By rcorbett
get read position from Samtools pileup

Hi all,
Has anyone come across a way to get information about the location of a snp within the reads? I have the usual bam/sam/pileup files.

For example,
r1: GAG
r2: GGG...
Forum: Bioinformatics 02-04-2010, 02:02 PM
Replies: 1
Views: 3,362
Posted By rcorbett
calling snps with samtools on novoalign data

Hi,
I have aligned illumina data with novoalign (default parameters). I directed novoalign to create SAM output. From here I am using samtools pileup/varfilter to call the snps.

I see that...
Forum: Bioinformatics 01-29-2010, 09:54 AM
Replies: 3
Views: 6,418
Posted By rcorbett
samtools flagstat mismatch in stats

Hi all,
I have a bam file created from illumina alignments with bwa. When I try to get the number of aligned reads 2 different ways I get 2 different numbers...

When I run flagstat:
samtools...
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