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Search: Posts Made By: lkral
Forum: Oxford Nanopore 05-18-2015, 12:56 PM
Replies: 10
Views: 3,382
Posted By lkral
Great, I'll look forward to it.

Great, I'll look forward to it.
Forum: Oxford Nanopore 05-18-2015, 08:46 AM
Replies: 10
Views: 3,382
Posted By lkral
Thanks. Full length reads are what I'm hoping for...

Thanks. Full length reads are what I'm hoping for and that fact that these are 2d reads bodes well for increased accuracy.
Forum: Oxford Nanopore 05-14-2015, 10:18 AM
Replies: 10
Views: 3,382
Posted By lkral
If anyone at the nanopore conference is reading...

If anyone at the nanopore conference is reading this, I would appreciate a bit more detail on mRNA sequencing. I assume this will be full length sequencing?
Forum: Oxford Nanopore 05-14-2015, 10:13 AM
Replies: 10
Views: 3,382
Posted By lkral
Can't wait for all this to go commercial

Looks like the sequencing world will be quite different in a year or two.

https://storify.com/OmicsOmicsBlog/london-calling-day-1
Forum: Bioinformatics 10-17-2014, 10:42 AM
Replies: 4
Views: 997
Posted By lkral
Depends how long the contigs are. It is likely...

Depends how long the contigs are. It is likely that even long contigs (over 10 Kb) will contain only partial genes. But as long as you are not trying to carry out whole genome comparisons you can...
Forum: Bioinformatics 10-17-2014, 06:03 AM
Replies: 4
Views: 997
Posted By lkral
Fgenesh worked very well for my needs as a first...

Fgenesh worked very well for my needs as a first step to identify potential genes. To actually annotate, fgenesh++ would be needed but I have not been able to try that out with my scaffolds (anyone...
Forum: Oxford Nanopore 10-07-2014, 05:19 PM
Replies: 47
Views: 15,316
Posted By lkral
If anyone in the MAP can talk about this, how...

If anyone in the MAP can talk about this, how does one prepare samples forMinION cDNA reads? Is it possible to get the entire length of the transcript sequenced or does the cDNA have to be fragmented...
Forum: The Pipeline 09-03-2014, 05:17 AM
Replies: 0
Views: 4,772
Posted By lkral
Oxford Nanopore user perspective

http://nextgenseek.com/2014/09/nick-lomans-talk-on-nanopore-sequencing-using-minion-at-ukgs2014/

Exciting stuff.
Forum: Bioinformatics 08-27-2014, 10:37 AM
Replies: 4
Views: 960
Posted By lkral
Thanks, GenoMax. That should do it. Geneious can...

Thanks, GenoMax. That should do it. Geneious can import SAM/BAM files. I have a Mac with 8 GB of RAM that should be able to handle this.

And yes, we have limited computing resources. Also, to...
Forum: Bioinformatics 08-27-2014, 05:32 AM
Replies: 4
Views: 960
Posted By lkral
Looking for appropriate software

I currently have a number of undergraduate students annotating genes within scaffolds of a particular fish species using WebApollo. I also have Illumina NextSeq PE150 reads from a closely related...
Forum: Bioinformatics 08-06-2014, 12:43 PM
Replies: 251
Views: 88,499
Posted By lkral
Thanks. I was hoping someone could verify that...

Thanks. I was hoping someone could verify that this worked before I started mucking with the system. Anyway, I did the install of the Perl4::CoreLibs module from CPAN and that fixed it.
Forum: Bioinformatics 08-06-2014, 07:24 AM
Replies: 251
Views: 88,499
Posted By lkral
Last year i was able to run SSPACE just fine. Now...

Last year i was able to run SSPACE just fine. Now I'm getting the "Can't locate getopt.pl in @INC…" error. Has anyone had success on a workaround? I'm on Mac OS X.

Thanks, Leos
Forum: Bioinformatics 05-08-2014, 06:56 AM
Replies: 24
Views: 11,947
Posted By lkral
I was able to use Geneious to assemble...

I was able to use Geneious to assemble mitochondrial DNA form Illumina reads of fish DNA but in a different way than that suggested by Matt Kearse. I started with a small number of mitochondrial...
Forum: General 02-18-2014, 07:02 AM
Replies: 13
Views: 4,818
Posted By lkral
I had done a number of long range PCRs up to 10KB...

I had done a number of long range PCRs up to 10KB from related species with a conserved pair of primers and I found that some enzymes and mixes worked and some did not. Funds permitting, you may want...
Forum: Bioinformatics 06-04-2013, 03:56 AM
Replies: 2
Views: 926
Posted By lkral
Thanks for the references. And to be clear,...

Thanks for the references.

And to be clear, there are 53 million individual reads.
Forum: Bioinformatics 06-02-2013, 02:53 PM
Replies: 2
Views: 926
Posted By lkral
Is this assembly reasonable?

I have completed some de novo assemblies of MiSeq generated 250PE reads with Minia and SSPACE. I've posted a description of the outcomes and some quality checks at the following site:
...
Forum: Bioinformatics 05-24-2013, 06:48 AM
Replies: 2
Views: 930
Posted By lkral
Geneious works very well for this. You just...

Geneious works very well for this. You just select the gene sequence and the list of reads and use the map to reference function.
Forum: Bioinformatics 02-21-2013, 08:32 AM
Replies: 2
Views: 847
Posted By lkral
I missed this somehow, but the Gossamer readme...

I missed this somehow, but the Gossamer readme file says:

"Mammalian size genomes have been assembled using goss on a 32 GB Ubuntu machine."

So, since the genome I'll be assembling is about 1...
Forum: Bioinformatics 02-20-2013, 11:40 AM
Replies: 2
Views: 847
Posted By lkral
GOSSAMER hardware recommendation?

I will need to assemble a genome from two PE250 MiSeq runs generating a total of about 12 to 14 Gbp of sequence. Based on some preliminary alignments to genes I had previously cloned and sequenced...
Forum: General 05-14-2012, 09:40 AM
Replies: 6
Views: 2,334
Posted By lkral
I am patiently waiting for the MinION to come...

I am patiently waiting for the MinION to come out. I also want to sequence ~10 kb PCR products and obtain full allele sequences.
Forum: Bioinformatics 03-31-2012, 11:58 AM
Replies: 10
Views: 2,170
Posted By lkral
The current project is phase I where all I need...

The current project is phase I where all I need to do is obtain contigs that are large enough to contain a gene or part of a gene. If contigs are smaller than a gene I can align these to orthologs...
Forum: Bioinformatics 03-30-2012, 06:11 AM
Replies: 10
Views: 2,170
Posted By lkral
Thank you all. I'll play it safe and with a 500...

Thank you all. I'll play it safe and with a 500 to 600 bp library.
Forum: Bioinformatics 03-28-2012, 06:14 AM
Replies: 10
Views: 2,170
Posted By lkral
de novo assembly of PE reads

I am about to have DNA sequenced on a HiSeq and I expect about a 30 fold coverage of a 1x10^9 bp genome with 100 bp PE reads. I am unsure of the size of the fragments I should use to get the best...
Forum: Illumina/Solexa 09-13-2011, 06:34 AM
Replies: 7
Views: 2,538
Posted By lkral
The approach I was thinking of was to use tblastn...

The approach I was thinking of was to use tblastn to pull out the Illumina obtained sequences that correspond to the exons of the genes of interest, "pin" these in place in the proper order and in...
Forum: Illumina/Solexa 09-13-2011, 06:23 AM
Replies: 7
Views: 2,538
Posted By lkral
Thanks for the reference. An approach worth...

Thanks for the reference. An approach worth exploring.
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