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Search: Posts Made By: gavin.oliver
Forum: General 04-30-2012, 01:14 AM
Replies: 2
Views: 3,459
Posted By gavin.oliver
Hi, The project fell by the wayside in the...

Hi,

The project fell by the wayside in the end unfortunately.

I heard numerous claims that DSN normalization works very well but only in the right hands - it seems to be a temperamental...
Forum: Bioinformatics 04-24-2012, 08:37 AM
Replies: 0
Views: 1,079
Posted By gavin.oliver
What is your approach to variant filtering?

While looking at some exome data I was struck by how widely my final variant list varies using different approaches. Using variant score reclalibration alone with GATK I ended up with 40,000...
Forum: General 02-29-2012, 02:55 PM
Replies: 51
Sticky: NGS Blogs
Views: 48,122
Posted By gavin.oliver
Thanks Dan! I look forward to discussing things...

Thanks Dan! I look forward to discussing things further.
Forum: General 02-29-2012, 11:34 AM
Replies: 51
Sticky: NGS Blogs
Views: 48,122
Posted By gavin.oliver
A lot of great blogs on this list. I made it...

A lot of great blogs on this list.

I made it a resolution for 2012 to start a sequencing-related blog. Have a look. (Constructive) criticism is welcome :)
...
Forum: Bioinformatics 01-09-2012, 12:52 AM
Replies: 14
Views: 3,151
Posted By gavin.oliver
Nils, RE the second read name - it must have been...

Nils, RE the second read name - it must have been a copy/paste error as the file actually does contain it:

@chr17:95861:F:237/1...
Forum: Bioinformatics 01-06-2012, 01:30 AM
Replies: 14
Views: 3,151
Posted By gavin.oliver
Nils, I interleaved the two files and have...

Nils,

I interleaved the two files and have run them using Bfast. However, whenever I reach the postprocess stage, I am not getting successful pairing of the reads regardless of what I specify on...
Forum: Bioinformatics 01-05-2012, 05:15 AM
Replies: 14
Views: 3,151
Posted By gavin.oliver
Thanks Nils - I'll write something to interleave...

Thanks Nils - I'll write something to interleave the two files.
Forum: Bioinformatics 01-04-2012, 03:58 AM
Replies: 14
Views: 3,151
Posted By gavin.oliver
Using Bfast to align paired end Illumina reads

Hi,

I am attempting to align paired end Illumina reads to the human genome with Bfast.

The problem is that most aligners expect paired end reads in 2 fastq files while Bfast expects 1 file. ...
Forum: Bioinformatics 12-08-2011, 01:03 AM
Replies: 1
Views: 1,068
Posted By gavin.oliver
Bfast, single end reads and large indels

Hi,

I am wondering what the largest indels I can theoretically detect with Bfast and single end 90bp reads are? Has anyone got experience in this? Come on Nils - I know you must have :D
Forum: Bioinformatics 12-06-2011, 12:52 AM
Replies: 7
Views: 3,289
Posted By gavin.oliver
This particular dataset is all single end. I am...

This particular dataset is all single end. I am pretty certain the larger indels can still be detected though...
Forum: Bioinformatics 12-05-2011, 08:23 AM
Replies: 7
Views: 3,289
Posted By gavin.oliver
I am pretty sure my commands are very standard. ...

I am pretty sure my commands are very standard. Nonetheless, you are welcome to have a look!

for file in *fastq; do bwa aln -e 50 -f ${file%%.fastq}.sai chr17hg19 ${file}; done

for file in...
Forum: Bioinformatics 12-05-2011, 06:40 AM
Replies: 7
Views: 3,289
Posted By gavin.oliver
Indeed I do.

Indeed I do.
Forum: Bioinformatics 12-05-2011, 03:48 AM
Replies: 7
Views: 3,289
Posted By gavin.oliver
I am now getting all Indels up to 29bp in length....

I am now getting all Indels up to 29bp in length. I achieved this by increasing the maximum number of permitted gap extensions with bwa aln -e 50.

I will continue to experiment in order to get...
Forum: Bioinformatics 12-05-2011, 01:23 AM
Replies: 7
Views: 3,289
Posted By gavin.oliver
6-99bp indels with BWA/GATK

Hi,

I am using BWA and GATK to detect mutations in BRCA1. The BRCA1 sequences have been Sanger validated and contain known mutations. I am achieving a fair degree of accuracy so far,...
Forum: Bioinformatics 11-30-2011, 03:16 AM
Replies: 3
Views: 1,949
Posted By gavin.oliver
BEDTools appears to be what I am after - cheers!

BEDTools appears to be what I am after - cheers!
Forum: Bioinformatics 11-29-2011, 08:15 AM
Replies: 3
Views: 1,949
Posted By gavin.oliver
Comparing and combining vcf files

Hi,

I am trying to determine if there is an available solution for comparing vcf files and combining them into a single, non-redundant file?

So for example, if I have two vcf files for two...
Forum: Ion Torrent 11-22-2011, 04:46 AM
Replies: 1
Views: 1,292
Posted By gavin.oliver
Sequence biases toward read ends

I'm just having a look at the publicly available DH10B data with the FastQC program and notice some pretty huge spikes in sequence bias at the 3' end, with smaller rises at the 5` end. Being new to...
Forum: General 11-10-2011, 07:57 AM
Replies: 3
Views: 2,860
Posted By gavin.oliver
Nick, can I just follow this up? Between...

Nick, can I just follow this up?

Between MiSeq and Ion Torrent - which do you see having the greater clinical application (generally)?

Also, more specifically are the homopolymers likely to be...
Forum: General 11-09-2011, 12:52 AM
Replies: 3
Views: 2,860
Posted By gavin.oliver
Thanks a lot for the input Nick - it's a great...

Thanks a lot for the input Nick - it's a great help.
Forum: General 11-08-2011, 02:45 AM
Replies: 3
Views: 2,860
Posted By gavin.oliver
SNP/Indel analysis and homopolymer errors

Hi,

I am wondering what the general consensus is on SNP/Indel detection from resequencing data generated by homopolymer error-prone platforms like 454 and Ion torrent?

Off the top of my head I...
Forum: Bioinformatics 09-21-2011, 08:23 AM
Replies: 4
Views: 2,875
Posted By gavin.oliver
I may be wrong, but isn't the recalibrator just...

I may be wrong, but isn't the recalibrator just scoring your variants with a new metric? Therefore the filtering itself would still remain to be done based on the VQSLOD values?
Forum: Bioinformatics 09-15-2011, 02:59 AM
Replies: 0
Views: 787
Posted By gavin.oliver
Cufflinks deconvolution warnings and fpkm_tracking files

Hi all,

I am aware that deconvolution warnings in the isoforms.fpkm_tracking files generated by cufflinks mean the entry should be treated with suspicion/ignored.

However, am I correct in...
Forum: Polonator 08-15-2011, 12:45 AM
Replies: 11
Views: 53,106
Posted By gavin.oliver
Apparently the Polonator is no longer being sold...

Apparently the Polonator is no longer being sold but customers are being offered upgrade to the new Max-Seq.
Forum: General 08-13-2011, 05:14 AM
Replies: 6
Views: 2,210
Posted By gavin.oliver
Approximately 50 samples for the purpose of...

Approximately 50 samples for the purpose of SNP/Indel analysis and genotyping. I had assumed 454 technology would be no good here because of the Indels. So it's OK to use traditional PCR approaches...
Forum: De novo discovery 08-12-2011, 05:22 AM
Replies: 3
Views: 1,801
Posted By gavin.oliver
Coverage required for Sanger based SNP detection and Genotyping

Does anyone know of an established acceptable figure in terms of times coverage required for SNP/calling and genotyping with Sanger sequences?

I know 20x is generally recommended for NGS but this...
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