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Search: Posts Made By: lg36
Forum: Bioinformatics 06-05-2012, 08:15 AM
Replies: 3
Views: 1,769
Posted By lg36
Thanks Seb that's helpful. My peaks do overlap...

Thanks Seb that's helpful. My peaks do overlap in the sense that the frequency of the paired end reads does not drop to zero between the peaks. This is an assembly of a single bacteria. The median...
Forum: Bioinformatics 06-03-2012, 07:17 PM
Replies: 1
Views: 1,199
Posted By lg36
How to best use my lab data to check my alignment??

Dear All,

These are three different pipelines I've used to call SNPs on the same samples:

1) Raw FastQ File --> Direct Mapping to Reference --> SNP discovered 1,200

2) Raw FastQ File --> De...
Forum: Bioinformatics 06-02-2012, 12:38 PM
Replies: 5
Views: 1,782
Posted By lg36
Thanks both so much for your help. Just to give...

Thanks both so much for your help. Just to give you some more information, the second method gives me a consensus sequence which is most representative of the consensus sequence we have already...
Forum: Bioinformatics 06-01-2012, 06:27 PM
Replies: 5
Views: 1,782
Posted By lg36
Which Pipeline is Correct??

Dear All,

I'd be very grateful for any advice on which (if any) of the following processes to take for SNP discovery? I find a different number of SNPs with each approach with the same SNP...
Forum: Bioinformatics 05-31-2012, 11:24 AM
Replies: 2
Views: 1,403
Posted By lg36
Thanks pag for your help. So, is it true to say...

Thanks pag for your help. So, is it true to say if I can replicate what we know to be the reality of the consensus sequence (from our lab findings), then the SNPs that are output from the same...
Forum: Illumina/Solexa 05-31-2012, 10:59 AM
Replies: 0
Views: 6,546
Posted By lg36
bimodal paired end width distribution illumina

Hi All,

What does a bimodal paired end width distribution imply when dealing with illumina paired end files??

Best wishes

lg36
Forum: Bioinformatics 05-31-2012, 10:36 AM
Replies: 2
Views: 1,403
Posted By lg36
Please Help - SNP Calling in relation to Consensus Sequence Quality

Dear All,

I've posted on this before and attracted no interest at all. So I'd be very grateful to get your opinions. I'm relatively new to NGS sequence analysis so apologies for any naive...
Forum: Bioinformatics 05-30-2012, 07:29 AM
Replies: 3
Views: 1,769
Posted By lg36
Paired End Read Distribution Width for Similar Bacteria

Dear All,

The consensus sequence I produce differs significantly based on the paired end distribution width I choose.

My paired end distribution is bi-modal with a smaller wider peak at around...
Forum: Bioinformatics 05-30-2012, 07:07 AM
Replies: 1
Views: 1,521
Posted By lg36
Does a reliable consensus mean more reliable SNPs?

Dear All,

I'm relatively new to WGS analysis so please excuse any naivety on my part.

Before getting the WGS sequences I have confirmed the presence or absence of certain oligonucleotides in...
Forum: Bioinformatics 05-06-2012, 04:53 PM
Replies: 2
Views: 1,573
Posted By lg36
Thanks for your reply. I was wanting to...

Thanks for your reply.

I was wanting to somehow calibrate the SNP filters based on the correctness of the consensus sequence. I figured (perhaps incorrectly) that a reasonable test of the...
Forum: Bioinformatics 05-05-2012, 12:15 PM
Replies: 2
Views: 1,573
Posted By lg36
My unreliable consensus sequences with mpileup?

Dear All,

I've used (what I think are) default settings to align paired end Illumina data using bwa then samtools and finishing with mpileup.

Before obtaining my sequences I PCR'd all our...
Forum: Bioinformatics 03-15-2012, 09:33 PM
Replies: 3
Views: 2,708
Posted By lg36
Viewing vcf and bam files in artemis

Dear All, I'm new to Artemis and could do with some help viewing vcf files.

1) First I loaded my embl reference file
2) Then I index my vcf files with tabix as per the manual
3) Then I go to...
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