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Search: Posts Made By: AdrianP
Forum: Bioinformatics 04-26-2015, 12:51 PM
Replies: 252
Views: 107,815
Posted By AdrianP
looks like you need sudo rights, but it's odd...

looks like you need sudo rights, but it's odd that you need permission to write in your own home directory.
Forum: Bioinformatics 04-26-2015, 12:42 PM
Replies: 252
Views: 107,815
Posted By AdrianP
what about sudo make install?

what about sudo make install?
Forum: Bioinformatics 04-26-2015, 12:36 PM
Replies: 252
Views: 107,815
Posted By AdrianP
was the installation successful? Or did it give...

was the installation successful? Or did it give errors? Are you using perlbrew by any chance?
Forum: Bioinformatics 04-26-2015, 12:30 PM
Replies: 252
Views: 107,815
Posted By AdrianP
Hello, see if this helps: sudo cpan install...

Hello, see if this helps:
sudo cpan
install Perl4::CoreLibs
Forum: Bioinformatics 04-14-2015, 02:28 PM
Replies: 11
Views: 5,495
Posted By AdrianP
This script is amazing! Is there any way to write...

This script is amazing! Is there any way to write a pipeline where it can serially check the SRA reads for a particular locus, that is check them individually? Also, the output is XML, is there...
Forum: Bioinformatics 12-10-2014, 05:52 PM
Replies: 58
Views: 13,132
Posted By AdrianP
Thanks for clarifying that. I am having real...

Thanks for clarifying that. I am having real trouble installing the software:

@BioPower3-IBM ~/programs/meraculous-2.0.4 $ export Boost_INCLUDE_DIRS=/home/adrian/programs/boost_1_55_0/boost/...
Forum: Bioinformatics 12-08-2014, 05:08 PM
Replies: 58
Views: 13,132
Posted By AdrianP
You sure about that? Is this the assembler? ...

You sure about that?

Is this the assembler?
https://registry.hub.docker.com/u/egoltsman/meraculous2-docker/
Forum: Bioinformatics 09-10-2014, 09:35 AM
Replies: 0
Views: 867
Posted By AdrianP
Loss of Heterozygosity from VCF file in non-model organisms

If I have a .vcf file showing positions with variation, how can I find regions that exhibit the lowest amount of SNP density, perhaps due to LOH? In this case copy number should be irrelevant, as...
Forum: Bioinformatics 09-10-2014, 09:32 AM
Replies: 0
Views: 822
Posted By AdrianP
Anyone know of Tetraploid NGS available?

Hello,

I am trying to interpret my k-mer graph which indicates that my organism might be tetraploid. However, I cannot find any good tetraploid NGS data to compare to. All plants are usually...
Forum: Bioinformatics 09-03-2014, 09:32 AM
Replies: 13
Views: 18,530
Posted By AdrianP
I am going to try this solution now as I have the...

I am going to try this solution now as I have the same issue.
Forum: Bioinformatics 06-14-2014, 09:16 PM
Replies: 3
Views: 2,816
Posted By AdrianP
I am more interested in events between strains....

I am more interested in events between strains. The data shows the organism is clonal, so the strain can be treated as an individual, most variation is due to ploidy. My coverages range from 120x to...
Forum: Bioinformatics 06-14-2014, 06:26 PM
Replies: 3
Views: 2,816
Posted By AdrianP
Test for recombination in a clonal tetraploid?

I have been searching this subject and trying to find a technique that fits my needs and so far I have been having no success.

I am looking to test try and find crossover events in my HiSeq...
Forum: Bioinformatics 06-14-2014, 06:24 PM
Replies: 252
Views: 107,815
Posted By AdrianP
Give it a few days before bumping please.

Give it a few days before bumping please.
Forum: Bioinformatics 05-16-2014, 02:03 PM
Replies: 0
Views: 656
Posted By AdrianP
Recombination from phased data

Hello,

I am using NGS to obtain data from a couple of isolates of one species. The isolates seem to be very similar to each other, sharing a lot of genetic variation (SNPs).

I managed to phase...
Forum: Bioinformatics 04-21-2014, 09:45 AM
Replies: 58
Views: 13,132
Posted By AdrianP
Very interesting! Too bad the polymorphic genomes...

Very interesting! Too bad the polymorphic genomes are a tough cookie. Indeed the one I am currently working with has at least 1 polymorphic region every 100bp, every read. So normalizations can...
Forum: Bioinformatics 04-20-2014, 10:35 AM
Replies: 58
Views: 13,132
Posted By AdrianP
This sounds really cool! Now if the data is...

This sounds really cool!

Now if the data is MiSeq and the 250bp reads overlap, should I perform merging first?

Also, what coverage do you suggest the normalization to take place? is 50x enough?...
Forum: Bioinformatics 04-20-2014, 06:28 AM
Replies: 58
Views: 13,132
Posted By AdrianP
Sorry to ask this here, but where can I find more...

Sorry to ask this here, but where can I find more about BBNorm, and what exactly does k-mer normalization do?
Forum: Bioinformatics 04-15-2014, 03:40 PM
Replies: 1
Views: 987
Posted By AdrianP
Anyone? (bump)

Anyone? (bump)
Forum: Bioinformatics 04-14-2014, 04:08 PM
Replies: 6
Views: 3,224
Posted By AdrianP
I have never heard of your initial idea of...

I have never heard of your initial idea of demultiplexing based on similarity. That's essentially what an assembler does, separates reads based on which reads form contigs...

There is no proof of...
Forum: Bioinformatics 04-13-2014, 05:58 PM
Replies: 6
Views: 3,224
Posted By AdrianP
As long as your PCR product are overlapping, you...

As long as your PCR product are overlapping, you should be fine. Indeed you can just denovo assemble it by feeding it the entire library. Assemble each library individually.

As a side thing, you...
Forum: Bioinformatics 04-13-2014, 01:22 PM
Replies: 1
Views: 987
Posted By AdrianP
Detecting Recombination from NGS polyploid data

Hello,

I have a clonally propagating fungus that I am resequencing from different geographic locations. Since it is thought to be clonal, I expect very little or no recombination happening,...
Forum: Bioinformatics 04-13-2014, 01:15 PM
Replies: 6
Views: 3,224
Posted By AdrianP
All you want is mtDNA right? Just assemble...

All you want is mtDNA right?

Just assemble it w/o demultiplexing, you should get mtDNA contigs for each of your taxa.

How long is your fragment size? With MiSeq + your situation I recommend...
Forum: Bioinformatics 04-13-2014, 07:09 AM
Replies: 12
Views: 5,646
Posted By AdrianP
Bold is solution.

Bold is solution.
Forum: Bioinformatics 04-12-2014, 06:39 PM
Replies: 3
Views: 2,149
Posted By AdrianP
and it is talking about alignment, so I believe...

and it is talking about alignment, so I believe the error relates to the .bam file?
Forum: Bioinformatics 04-12-2014, 06:13 PM
Replies: 3
Views: 2,149
Posted By AdrianP
I have NNNN in my sequences and it runs just...

I have NNNN in my sequences and it runs just fine.

Is that a "\" i see in your sequence?
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