SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 14 of 14
Search took 0.00 seconds.
Search: Posts Made By: BertieWooster
Forum: Bioinformatics 12-30-2014, 02:32 AM
Replies: 0
Views: 1,083
Posted By BertieWooster
Question Known Sites for GATK's BQSR for non-human data

Hello,

I am working on non-human data and want to use GATK's Haplotype caller to call variants. I am using the protocol that is listed here...
Forum: General 12-11-2014, 01:54 AM
Replies: 1
Views: 1,346
Posted By BertieWooster
Question Error Message when running bwa 0.7.10

Hello,

I get the following error message when I try using bwa/0.7.10:

BWTIncConstructFromPacked() : Can't read from MyGenome.fa.pac : Unexpected end of file

Has anybody else encountered the...
Forum: Bioinformatics 04-03-2013, 03:51 PM
Replies: 0
Views: 857
Posted By BertieWooster
Question BWA Alignments missing regions

Hello,

I have a very short gene sequence that I have appended to my reference assembly as a "new" chromosome. I have then aligned the new assembly to a set of 101 PE Illumina reads using BWA;...
Forum: Bioinformatics 09-24-2012, 07:51 AM
Replies: 1
Views: 1,719
Posted By BertieWooster
Question Aligned position within a read from Samtools mpileup

Hello,

Is it possible to infer the aligned position within a read (1-101) of every read in the alignment from a mpileup file?

Thanks for your input!

~BW
Forum: Bioinformatics 06-20-2012, 04:25 PM
Replies: 1
Views: 1,197
Posted By BertieWooster
Question GASVpro - Input files and quick start guide?

Hello,

What are the input files required to run the tool GASVpro. I have run the example provided, but the manual does not elaborate on what files and the format in which they are needed?
...
Forum: Bioinformatics 06-07-2011, 10:34 AM
Replies: 0
Views: 2,500
Posted By BertieWooster
Question CNVnator for Non-human data

Hello,

Does anyone have experience with running CNVnator for non-human data?

I have installed the root package as recommended. However, I keep getting the following error:

Error in...
Forum: Bioinformatics 04-25-2011, 11:55 AM
Replies: 10
Views: 2,701
Posted By BertieWooster
Question Pileup shows variants - Not called as SNPs

Hello,

I notice that with samtools pileup/mpileup, there are several positions which have variants that can be classified as SNPs. However, they fail to show up when using the subsequent SNP...
Forum: Bioinformatics 02-08-2011, 04:25 PM
Replies: 0
Views: 1,703
Posted By BertieWooster
Question GC Cover versus mapped depth

Hello,

A rather naive question:

I would like to compute the GC% versus mapped depth for contiguous sliding windows of 2000 bp. For the mapped depth do I just add the coverage at all GC...
Forum: Bioinformatics 10-20-2010, 06:19 PM
Replies: 5
Views: 3,335
Posted By BertieWooster
Question Samtools SNP Caller versus MAQ SNP caller

I have been using MAQ's variant caller to call SNPs. I now want to use Samtools.pl varfilter and want to make sure that I maintain the same conditions I had for MAQ. My question is which of the...
Forum: Bioinformatics 09-13-2010, 12:29 PM
Replies: 1
Views: 1,699
Posted By BertieWooster
Alignment Cover for Simulated Illumina Reads

Hello,

I generated 100 M reads using maq’s simulate and simutrain commands. Once I align the reads against an assembly, I note that I get a much higher coverage alignment-wise than if I were to...
Forum: Bioinformatics 06-09-2010, 09:25 AM
Replies: 0
Views: 2,210
Posted By BertieWooster
maq consensus sequence

What exactly does the maq consensus sequence contain?
Forum: Bioinformatics 12-11-2009, 08:23 AM
Replies: 3
Views: 1,811
Posted By BertieWooster
Well, the maq map output itself is binary. You...

Well, the maq map output itself is binary. You can run the pileup command to give you the read bases and the quality at each position. Check the maq documentation and that should elaborate further...
Forum: Bioinformatics 12-11-2009, 08:09 AM
Replies: 2
Views: 3,147
Posted By BertieWooster
Per Base Error Rate for Next-Gen Sequencing

Hiya,

Given an alignment coverage table data (for Next-Gen), how would one go about computing the per base error rate?

Thx,
Bertie
Forum: Bioinformatics 07-28-2009, 02:21 PM
Replies: 1
Views: 5,598
Posted By BertieWooster
Question Minor Allele Frequency Cutoff/Threshold

G'day,

I am writing to enquire what maf cutoff/threshold people use when getting snps using the maq snp caller or any other means.

A lot of researchers seem to use 0.05 as applied for HapMap,...
Showing results 1 to 14 of 14

 


All times are GMT -8. The time now is 08:06 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO