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Forum: Bioinformatics 05-26-2015, 06:19 AM
Replies: 147
Views: 58,199
Posted By BGould
pindel variants counted multiple times

Hi Hshain, I have this same issue using Pindel 0.2. Did you ever figure out why this is happening or how to fix/avoid this problem?
Forum: Bioinformatics 09-04-2014, 07:40 AM
Replies: 1
Views: 1,711
Posted By BGould
Pindel, pindel2vcf, AD for REF allele always zero?

Hello fellow Pindel users,
I am using Pindel to detect structural variants and I find that in output VCF files, the allele depth (AD) for the reference allele for all variants in all samples is...
Forum: Bioinformatics 01-07-2014, 05:58 AM
Replies: 0
Views: 2,022
Posted By BGould
what is the meaning of vcf-stats output for shared snps??

this was answered . . .

One of the output files of vcf-stats tool, (*.shared), seems to indicate it counts only only sites where the samples of interest share a non-reference allele. Is this...
Forum: RNA Sequencing 06-06-2013, 06:31 PM
Replies: 1
Views: 1,134
Posted By BGould
Alignment Image attached

alignment image is attached here
Forum: RNA Sequencing 06-06-2013, 06:13 PM
Replies: 1
Views: 1,134
Posted By BGould
Can you explain this alignment coverage pattern?

Hello, I am visualizing RNA-seq PE reads using IGV and I see some strange but consistent patterns in the variation of depth of expression within some transcripts. I am aligning reads to a...
Forum: RNA Sequencing 10-04-2012, 07:04 AM
Replies: 5
Views: 2,802
Posted By BGould
Same problem, ad hoc fix anyone?

Hi, I had the same problem. I completed a large blast run and now have a .dat file only. Does anyone have a way to generate an xml output file from the .dat file? I can't find this anywhere in the...
Forum: Bioinformatics 04-03-2012, 11:12 AM
Replies: 2
Views: 1,434
Posted By BGould
Thanks Wolfgang!

Thanks Wolfgang!
Forum: Bioinformatics 03-28-2012, 04:46 PM
Replies: 2
Views: 2,511
Posted By BGould
Should one combine normalization methods in RNA-seq?

Does anyone know if RPKM normalization and quantile normalization of RNA-seq read counts can or should be combined?

For normalization of paired-end reads in RNA-seq, is it accurate to normalize...
Forum: Bioinformatics 03-20-2012, 01:09 PM
Replies: 2
Views: 1,434
Posted By BGould
Independent point independence in RNA-seq?

Hi All,
I am in the midst of trying out different methods for measuring the statistical significance of gene expression levels in and RNA seq experiment. It seems like all the methods I come across...
Forum: Bioinformatics 03-18-2012, 07:49 AM
Replies: 1
Views: 3,828
Posted By BGould
Trinity Assembly, Isoforms vs. Paralogs?

Hello Everyone,
I am in the midst of going through a denovo non-model plant transcriptome assembly using Trintiy. I have so far been unable to find references on strategies for differentiating...
Forum: RNA Sequencing 05-26-2011, 12:58 PM
Replies: 4
Views: 2,780
Posted By BGould
Question Interspecies alignment and read length comparison?

I am planing on aligning RNASeq reads from a nonmodel plant to a model plant genome. Does anyone have experience with (or know of any great references) comparing the amount of alignment using short...
Forum: Illumina/Solexa 03-23-2011, 11:49 AM
Replies: 9
Views: 9,025
Posted By BGould
Related Hi-seq Barcode issues?

Hi All,
I'm attempting to run barcoded libraries multiplexed on the Hi-seq platform, and I have had multiple failed runs. I have been trying to follow your thread here, but I'm relatively new to NGS...
Forum: RNA Sequencing 05-11-2010, 12:31 PM
Replies: 3
Views: 2,977
Posted By BGould
Red face Thanks!

thanks Pascal, this study is just what I was looking for. very comprehensive too. many thanks .:o
Forum: RNA Sequencing 05-05-2010, 07:53 AM
Replies: 3
Views: 2,977
Posted By BGould
Question house-keeping genes in RNA-seq data sets?

Hi All,
Does anyone out there know of a good reference or two on the depth of coverage required to cover most transcripts and gauge expression levels in RNA-seq experiments? In particular, can...
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