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Forum: Bioinformatics 06-14-2012, 05:04 AM
Replies: 1
Views: 1,666
Posted By Lspoor
SOAPddenovo v1.05 error-Cannot open output_prefix.kmerFreq.

Hello,

We are using SOAPdenovov1.05 on paired end 36bp Illumina reads with this command:
[s0977659@ris-lx03 bin]$ ./SOAPdenovo-31mer all -p 4 -s...
Forum: Bioinformatics 10-26-2011, 07:03 AM
Replies: 21
Views: 12,549
Posted By Lspoor
Hi kmcarr, Thank you for your reply regarding my...

Hi kmcarr, Thank you for your reply regarding my questions and apologies for the delayed response. According to the bioinformaticians that also initially quality checked our data this is the reply I...
Forum: Bioinformatics 10-24-2011, 08:43 AM
Replies: 3
Views: 8,933
Posted By Lspoor
I think the dots in the VCF are classed as a...

I think the dots in the VCF are classed as a missing values, which I think is because I've generated a VCF file for all sites, rather than just the variants, so it includes regions of invariant sites...
Forum: Bioinformatics 10-24-2011, 08:19 AM
Replies: 3
Views: 6,369
Posted By Lspoor
Question vcfutils.pl -specifying minimum read depth?

:confused:

Hi everyone, I was wondering if you might be able to help me with specifying a minimum read depth when calling consensus sequences?

I'm running samtools-0.1.18 on Ubuntu 10.04. I...
Forum: Bioinformatics 10-06-2011, 08:40 AM
Replies: 3
Views: 8,933
Posted By Lspoor
Unhappy Problem calling consensus sequence with Samtools mpileup?

:confused:
Hi all, I hope someone can help, have you come across anything like this yourself? I have several bacterial strain BWA genome assemblies. I am using Samtools to call the consensus and...
Forum: Bioinformatics 06-24-2011, 08:42 AM
Replies: 17
Views: 47,347
Posted By Lspoor
Thanks I got that to work, now I have a BAM file...

Thanks I got that to work, now I have a BAM file containing an alignment made from single (mixed) reads (whose corresponding pair was not of good enough quality to include in the analysis), so they...
Forum: Bioinformatics 06-24-2011, 07:55 AM
Replies: 17
Views: 47,347
Posted By Lspoor
OK Thanks, maybe I have duplicated reads...

OK Thanks, maybe I have duplicated reads somewhere? I'll try sorting the files before merging them and see if I get anywhere.
Forum: Bioinformatics 06-24-2011, 07:30 AM
Replies: 17
Views: 47,347
Posted By Lspoor
Unhappy extracting unmapped reads from BAM using Samtools?

Hi, I am trying to extract unmapped reads from my BWA sorted BAM file (paired end reads);

First I filter for the following things using these command lines which seems to work fine:
1) An...
Forum: Bioinformatics 06-10-2011, 09:46 AM
Replies: 2
Views: 2,646
Posted By Lspoor
Fixed!

And I just realised if I specified the path to samtools.p it worked! PLease delete my thread as it is no longer needed!
Forum: Bioinformatics 06-10-2011, 07:06 AM
Replies: 2
Views: 2,646
Posted By Lspoor
Red face samtools.pl pileup2fq problem?

Hi,

I am new to Samtools, and have a problem which I think must be simple to fix!

I am trying to use the following command on my dataset as per the manual:
$ samtools pileup -cf ref.fa aln.bam...
Forum: General 01-18-2011, 08:33 AM
Replies: 1
Views: 3,171
Posted By Lspoor
Question How to align SNP coordinates against a circular reference genome?

I have a list (tab-delimited file) of approximately 18 000 SNP coordinates for a bacterial reference genome GenBank file (When compared to one other query FASTA genome sequence using "dnadiff"...
Forum: Bioinformatics 06-05-2010, 06:23 AM
Replies: 50
Views: 22,810
Posted By Lspoor
I have freeglut3-dev and assoc packages installed...

I have freeglut3-dev and assoc packages installed on the newest version of Ubuntu? Not sure if I need to try another type of GLUT-dev package?
Forum: Bioinformatics 06-04-2010, 09:35 AM
Replies: 50
Views: 22,810
Posted By Lspoor
Thanks, I'll have a go!

Thanks, I'll have a go!
Forum: Bioinformatics 06-04-2010, 08:18 AM
Replies: 50
Views: 22,810
Posted By Lspoor
Question integrative genome viewer

Hi I had a look at this but from what I could see I could only choose from the listed genomes? Mine wasn't in there and I couldn't see a way of uploading your own genome in there?

I'm aligning...
Forum: Bioinformatics 06-04-2010, 07:16 AM
Replies: 50
Views: 22,810
Posted By Lspoor
SImilar problem in Maqview installation

Iam also getting the following error when typing in the "make" command as the last step to install the latest version of MAQVIEW, does anyone know what it means?

g++ -g -O2 -o maqview...
Forum: Bioinformatics 06-04-2010, 07:14 AM
Replies: 50
Views: 22,810
Posted By Lspoor
Same problem but still no joy following the answer to the thread

I had the same problem as Albert N. I followed the instructions in the thread. MaqView is trying to install and the initial configuration seems to go ok but I get the following error messages after I...
Forum: Bioinformatics 06-04-2010, 02:55 AM
Replies: 21
Views: 12,549
Posted By Lspoor
Question Newbie questions regarding Illumina read quality statistics using FASTX toolkit

I'm pretty new to NGS. I have Illumina GAII 36bp paired reads for several bacterial genomes. The sequencing was carried out in one run, using 2 lanes.
I have been using FASTX toolkit to produce...
Forum: Introductions 03-19-2010, 05:04 AM
Replies: 0
Views: 1,131
Posted By Lspoor
Hello from Edinburgh!

Glad I stunbled across this, trying to navigate my way through NGS for the next 3 years and this could well make a huge difference to me!
Thanks,
Laura
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