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Forum: Bioinformatics 02-18-2017, 09:58 AM
Replies: 0
Views: 1,541
Posted By sells78
Imterpretting BAYENV2

Hi all,
I've been trying to identify signatures of selection across a climate gradient using around 1000 SNPs and 15 populations.
This programme accepts that there is an element of noise from any...
Forum: Bioinformatics 01-30-2017, 06:28 AM
Replies: 4
Views: 1,975
Posted By sells78
Many thanks for such a prompt response. Best...

Many thanks for such a prompt response.

Best wishes
Forum: Bioinformatics 01-30-2017, 06:05 AM
Replies: 4
Views: 1,975
Posted By sells78
Hi Genomax, Thank you for the reply and my...

Hi Genomax,

Thank you for the reply and my apologies for what was aa badly worded and punctuated question.

I have a genome that I have built that is currently in fasta.gz format. I have to...
Forum: Bioinformatics 01-30-2017, 05:55 AM
Replies: 4
Views: 1,975
Posted By sells78
.fasta to .fsa conversion

Hi all,

Could someone kindly help me.

Does conversion of .fasta.gz after unzipping to.fsa, require a conversion by software or just a manual rename of end format?


Many thanks
Forum: Bioinformatics 09-13-2016, 08:38 AM
Replies: 1
Views: 1,039
Posted By sells78
Bowtie2 - how many output sam files?

Hi all,

My query is 'should bowtie 2 produce a separate SAM file for each pair of input reads from different samples?'

When specifying -1 and -2 and comma separated lists of input file for read...
Forum: Bioinformatics 09-12-2016, 01:23 PM
Replies: 0
Views: 920
Posted By sells78
Refernce allignment query in bowtie2

Hi all,

Apologies for what I'm sure are basic questions but if you have a reference sequence and a number of other genomes sequenced from the same species, one can align these in bowtie 2. The...
Forum: Bioinformatics 03-04-2016, 07:17 AM
Replies: 7
Views: 1,820
Posted By sells78
Hi Geno and Jessica, Apologies for the late...

Hi Geno and Jessica,

Apologies for the late thanks for your inputs into the query - very much apreciated.

It seems the issue I've had is the default match in cutadapt is 3 between sequence and...
Forum: Bioinformatics 02-22-2016, 04:17 AM
Replies: 7
Views: 1,820
Posted By sells78
Hi genomax, so samples have already been...

Hi genomax,
so samples have already been demultiplexed into libraries of 24 individuals and we have 30 libraries each with separate read 1 and read 2 files. I'm trying to run adapter removal on the...
Forum: Bioinformatics 02-22-2016, 02:53 AM
Replies: 7
Views: 1,820
Posted By sells78
Hi genomax - appreciate the response. could...

Hi genomax - appreciate the response.

could you possibly expand on what you mean by splitting them?

Many thanks

Jamie
Forum: Bioinformatics 02-21-2016, 11:24 AM
Replies: 7
Views: 1,820
Posted By sells78
cutadapt and barcode sequences

Hi all,

I'm trying to trim 125bp PE illumina reads with cutadapt to remove reads with any adapter sequence presence and then keep PE reeds which have no adapter or barcode readthrough.

I've run...
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