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Search: Posts Made By: danova
Forum: Bioinformatics 10-27-2016, 07:23 AM
Replies: 2
Views: 1,789
Posted By danova
Not looking for SNP , just the HSp proteins that...

Not looking for SNP , just the HSp proteins that are very conserved across species.
Forum: Bioinformatics 10-26-2016, 10:33 AM
Replies: 2
Views: 1,789
Posted By danova
PCR amplicons primer design - need advice

Hello,
I have a list of dna sequences corresponding to a family of HSP proteins in Bacteria (800 seqs of length average 570nt). I would like to design PCR primers for miseq amplification (2*250pb)....
Forum: Bioinformatics 10-13-2016, 07:39 AM
Replies: 4
Views: 3,072
Posted By danova
I found this script useful to retrain SILVA. ...

I found this script useful to retrain SILVA.

https://github.com/geraldinepascal/FROGS/blob/master/libexec/silva2retrainRDP.py
Forum: Bioinformatics 02-23-2016, 11:27 PM
Replies: 3
Views: 1,418
Posted By danova
thanks for the tips

thanks for the tips
Forum: Bioinformatics 02-23-2016, 07:48 AM
Replies: 3
Views: 1,418
Posted By danova
bbmerge mismatched

Hi,
While merging 16S pair-ended miseq data (2x250) i would like to disable ambiguous bases. BBmerge documentation states the following "When there is a mismatch, the base chosen is the one with the...
Forum: Illumina/Solexa 02-22-2016, 05:03 AM
Replies: 5
Views: 1,888
Posted By danova
Try with bbmerge: bbmerge.sh in1=file.R1.fq.gz...

Try with bbmerge:
bbmerge.sh in1=file.R1.fq.gz in2=file.R2.fq.gz out=file.merged.fq.gz outu1=files.unmerged.R1.fq.gz outu2=file.unmerged.R2.fq.gz merge=t mininsert=300 qtrim2=t minq=20

Play with...
Forum: Illumina/Solexa 02-22-2016, 12:40 AM
Replies: 5
Views: 1,888
Posted By danova
It looks like you have a problem with your...

It looks like you have a problem with your dataset. Illumina miseq chemistry for (2x300pb) is known to give unpredictable results. We have switched back to 2x250 as we had similar problems to yours...
Forum: Bioinformatics 02-16-2016, 10:58 AM
Replies: 2
Views: 1,714
Posted By danova
Thanks Brian, thats more clear now !!!

Thanks Brian, thats more clear now !!!
Forum: Bioinformatics 02-15-2016, 12:07 AM
Replies: 2
Views: 1,714
Posted By danova
bbmerge ratiomode ?

Hi,
bbmerge seems to use by default the ratiomode as follows:

ratiomode=t Newer algorithm. Slower, but higher merge rate.
Much better for long overlaps and high...
Forum: Metagenomics 02-09-2016, 12:40 AM
Replies: 3
Views: 2,832
Posted By danova
Scaffolding tools for metagenomics ???

Hello,
Im currently working on paired end data (2*150) to build a metagenomics assembly.

So far im using the combination of megahit to build contigs and soapdenovo for scaffolding. soapdenovo...
Forum: Bioinformatics 02-02-2016, 01:46 AM
Replies: 1
Views: 1,802
Posted By danova
bbduk for mirna mapping

Hi,
I have run a miseq run for microrna detection, filtered the data (removed adaptors and ncRNAs (others than microRNAs) and im now going to identify reads mapping to microRNAs in Human.

As for...
Forum: Bioinformatics 01-28-2016, 11:45 PM
Replies: 8
Views: 2,313
Posted By danova
Thanks Brian, Thanks for the masked version...

Thanks Brian,

Thanks for the masked version on Hg19. Do you hava also masked version hg38 ?

Just another quick question. Have you published BBmap or how to cite your software ?
Forum: Bioinformatics 01-28-2016, 04:38 AM
Replies: 8
Views: 2,313
Posted By danova
great ill work on that.... combining with...

great ill work on that.... combining with bbsplit
thanks
Forum: Bioinformatics 01-28-2016, 01:25 AM
Replies: 8
Views: 2,313
Posted By danova
Sorry for the confusion. I was confused with...

Sorry for the confusion. I was confused with large blast databases (.nal file). bbduk does its own indexing....so no way to use blast index databases.

Which Human database does people mots...
Forum: Bioinformatics 01-28-2016, 12:45 AM
Replies: 8
Views: 2,313
Posted By danova
bbduk with a large reference database

Hi,
I would like to check for contaminants using both phiX and the human genome. My data is metagenomics data and i want to remove any read mapping to both phiX and the Human genome.

So far bbduk...
Forum: Pacific Biosciences 10-15-2015, 10:42 AM
Replies: 2
Views: 1,507
Posted By danova
thanks Brian, Looks like a good approach.

thanks Brian,
Looks like a good approach.
Forum: Pacific Biosciences 10-14-2015, 10:37 PM
Replies: 2
Views: 1,507
Posted By danova
bbmap error rate - subs - indels

HI,
Im running a pacbio experiment where im testing a mock against a set of pacbio reads.
Im looking for the error rate , subs, and indwells. Exactly like the Pacbioalign output.

Is it...
Forum: Pacific Biosciences 10-12-2015, 10:51 AM
Replies: 6
Views: 1,833
Posted By danova
Thanks, It looks to me that id better wait for...

Thanks,
It looks to me that id better wait for Pacbio to work on that and see how it improves over the time. Thanks for the update,
david
Forum: Pacific Biosciences 10-12-2015, 09:26 AM
Replies: 6
Views: 1,833
Posted By danova
Right I mixed a coupe of things here. Let me...

Right I mixed a coupe of things here. Let me explain better
1 / I have sequenced a community mock and generated the CSS. From the CSS i can define the error rate.
2 / Now, I would like to generate...
Forum: Pacific Biosciences 10-12-2015, 09:04 AM
Replies: 6
Views: 1,833
Posted By danova
Id like to aligne the subreads by other means...

Id like to aligne the subreads by other means and compare it to the obtained CSS from the pacbio and evaluate the error rate.
Dont know how to actually get the error rate as well as number of...
Forum: Pacific Biosciences 10-11-2015, 12:05 PM
Replies: 6
Views: 1,833
Posted By danova
Subreads alignment alternatives

Hi,
Just wondering if anybody has tried to align subreads and build the CCS using alternative alignements programs, others than Blasr.

Im thinking of bwa.
The problem is that if you are...
Forum: Bioinformatics 09-11-2015, 11:41 AM
Replies: 5
Views: 2,007
Posted By danova
Brian, That was really great and worked as...

Brian,
That was really great and worked as expected, however i need more control over the alignements. How can you count the number of mismatches (limit to 3 mismatches, with no indels)

Have...
Forum: Bioinformatics 09-10-2015, 12:30 PM
Replies: 5
Views: 2,007
Posted By danova
HI Brian, Im also working with Pacbio so...

HI Brian,
Im also working with Pacbio so definetly it looks pretty much close to what im trying to achieve. Im currently also evaluating pacbio primers and having the sam output is really...
Forum: Bioinformatics 09-10-2015, 11:50 AM
Replies: 5
Views: 2,007
Posted By danova
Hi Brian, At the end I want to see if my...

Hi Brian,
At the end I want to see if my degenrated primers (or the sum of the oligos as you suggest) match the same 16s. That will tell me the coverage of my primers in my 16s database.

Indeed...
Forum: Bioinformatics 09-10-2015, 07:13 AM
Replies: 5
Views: 2,007
Posted By danova
Bowtie2 - align two PCR primers help

Hi,
Not sure its the correct strategy by im trying to achieve the following:

1- I have two primers (see below) that map to 16s amplicons and they generate an insert of 1200 to 1400 nt long.
...
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