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Search: Posts Made By: Corydoras
Forum: Bioinformatics 07-11-2014, 05:33 AM
Replies: 1
Views: 907
Posted By Corydoras
Hi Marius, I realize this is a long shot,...

Hi Marius,

I realize this is a long shot, but I am trying to do something similar at the moment and was wondering how you went about identifying your haplotypes?

Thanks :)
Forum: Bioinformatics 07-11-2014, 04:21 AM
Replies: 0
Views: 641
Posted By Corydoras
Identifying unique alleles/haplotypes for contigs

Dear All,

I have successfully created contigs using paired-end RAD data, and equally successfully mapped raw reads from different species back to these contigs. So far so good and I am loving my...
Forum: Bioinformatics 06-30-2014, 02:59 AM
Replies: 16
Views: 4,076
Posted By Corydoras
Dear RAD/Assembly community, I was hoping I...

Dear RAD/Assembly community,

I was hoping I could pick your brains again regarding my assembly.
I normalized coverage and together with using velvetoptimiser I am quite happy with the results I...
Forum: Bioinformatics 06-20-2014, 01:06 AM
Replies: 24
Views: 7,675
Posted By Corydoras
Hi Brian, Thanks so much for that...

Hi Brian,

Thanks so much for that explanation :). I thought I wouldn't be able to go past 31 but it is best to double check.

Sorry as well for just deleting my post (and bombarding you with...
Forum: Bioinformatics 06-19-2014, 08:17 AM
Replies: 24
Views: 7,675
Posted By Corydoras
Hi Brian, That worked like a charm, thank...

Hi Brian,

That worked like a charm, thank you! The normalization also greatly improved the assemblies and the kmer-coverage distribution looks much nicer. I was just wondering: by default, bbnorm...
Forum: Bioinformatics 06-17-2014, 03:17 AM
Replies: 24
Views: 7,675
Posted By Corydoras
Hi Brian, I got a file with cleaned sequence...

Hi Brian,

I got a file with cleaned sequence data and I want to assemble this de-novo using velvet. Due to the nature of the sequencing and the library protocol, my kmer coverage is quite variable...
Forum: Bioinformatics 06-10-2014, 10:09 AM
Replies: 16
Views: 4,076
Posted By Corydoras
Thank you!! :)

Thank you!! :)
Forum: Bioinformatics 06-10-2014, 09:34 AM
Replies: 16
Views: 4,076
Posted By Corydoras
Thanks so much for your pointers, needless to say...

Thanks so much for your pointers, needless to say I would have not stumbled across any of them myself! (This is quite obviously my first NGS experience).

I am working with all at once, and naively...
Forum: Bioinformatics 06-10-2014, 02:59 AM
Replies: 16
Views: 4,076
Posted By Corydoras
Yes, I have read up on the fact that too high a...

Yes, I have read up on the fact that too high a coverage can cause issues and am keeping an eye out for that. I have not come across any 'kmer normalization scripts before', though I understand that...
Forum: Bioinformatics 06-09-2014, 05:32 AM
Replies: 16
Views: 4,076
Posted By Corydoras
Oh and also, I am assuming it would be best to...

Oh and also, I am assuming it would be best to combine all samples in one species to get better coverage in the assembly? Or is it common practice to assemble contigs for one individual at a time?
Forum: Bioinformatics 06-09-2014, 02:41 AM
Replies: 16
Views: 4,076
Posted By Corydoras
Thanks very much for this and sorry to have been...

Thanks very much for this and sorry to have been such a pain! This cleared things up for me enormously.

Yes, Stacks may indeed still be an option to assemble contigs for me, but I assume I could...
Forum: Bioinformatics 06-06-2014, 02:50 AM
Replies: 16
Views: 4,076
Posted By Corydoras
Thanks mastal for clarifying! However,...

Thanks mastal for clarifying!


However, Illumina itself says this in their leaflet on multiplexed sequencing processes: "Application Read 1 is generated using read 1 sequencing primer. The read...
Forum: Bioinformatics 06-06-2014, 02:13 AM
Replies: 16
Views: 4,076
Posted By Corydoras
Hi Eric! Thanks for your reply and first...

Hi Eric!

Thanks for your reply and first hand advice, it is really useful and much appreciated! My samples com from different species rather than different populations but I think Stacks may be...
Forum: Bioinformatics 06-05-2014, 07:39 AM
Replies: 16
Views: 4,076
Posted By Corydoras
Hi Mastal, Thanks for the quick reply, I...

Hi Mastal,

Thanks for the quick reply, I will have a look to make sure my understanding is correct :).

Well, 'long' is relative I guess :). Due to the random shearing step in RAD (and if my...
Forum: Bioinformatics 06-05-2014, 06:17 AM
Replies: 16
Views: 4,076
Posted By Corydoras
Velvet Assembly for PE RAD Sequences

Dear All,

I am currently working with a RAD sequencing data set, sequenced on a PE-150bp Hiseq and I am now wanting to assemble my data into wonderful and long contigs (all cleaned and...
Forum: Bioinformatics 06-04-2014, 08:54 AM
Replies: 188
Views: 51,885
Posted By Corydoras
Just in case anybody ever has a similar problem...

Just in case anybody ever has a similar problem or is confused and stumbles across my post:

Looking closer at my files and where the reverse adapter contamination occurred, it became obvious that...
Forum: Bioinformatics 06-04-2014, 08:48 AM
Replies: 3
Views: 1,409
Posted By Corydoras
Just in case anybody ever has a similar problem...

Just in case anybody ever has a similar problem or is confused and stumbles across my post:

Looking closer at my files and where the reverse adapter contamination occurred, it became obvious that...
Forum: Bioinformatics 05-29-2014, 09:38 AM
Replies: 3
Views: 1,409
Posted By Corydoras
Thank you very much for your quick reply! It is...

Thank you very much for your quick reply! It is much appreciated.
Forum: Bioinformatics 05-29-2014, 09:21 AM
Replies: 3
Views: 1,409
Posted By Corydoras
Data Clean & Adapter Contamination

Hello All,

I am currently starting to analyse my RAD data set (Illumina HiSeq, 150bp PE sequencing run). I have used Trimmomatic for the data clean and have checked for adapter contamination (as...
Forum: Bioinformatics 05-27-2014, 04:58 AM
Replies: 188
Views: 51,885
Posted By Corydoras
Hi, Sorry to hijack this post! I got...

Hi,

Sorry to hijack this post! I got paired-end 150bp RAD sequencing data that I am currently cleaning with Trimmomatic. I just have two quick questions to make sure I am not going wrong...
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