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Search: Posts Made By: dnusol
Forum: Bioinformatics 11-13-2014, 07:49 AM
Replies: 34
Views: 10,211
Posted By dnusol
Hi nielsk, are you still running into this...

Hi nielsk,

are you still running into this error?

If so, I am just trying out CONTRA for the first time so this may be of no help to you.

It seems CONTRA cannot find your .bed file in...
Forum: Bioinformatics 09-17-2014, 03:34 AM
Replies: 11
Views: 4,308
Posted By dnusol
Besides what gringer says, other options include...

Besides what gringer says, other options include commercial software such as dnastar or CLC suite, which may do the job with less amounts of RAM. At a cost, of course...
So it may be worth writing...
Forum: Bioinformatics 07-23-2014, 01:43 AM
Replies: 20
Views: 13,618
Posted By dnusol
Hi, we are seeing a similar issue using the...

Hi,

we are seeing a similar issue using the Agilent QXT kit, on captured and whole genome experiments. This kit also uses transposases.

HTH

Dave
Forum: Bioinformatics 07-21-2014, 08:32 AM
Replies: 1
Views: 1,547
Posted By dnusol
comparative metagenomics

hi all,

We are designing a comparative metagenomics experiment where we may run 3 different conditions with several individuals per condition. I am trying to see what would be an appropriate way...
Forum: Bioinformatics 02-25-2014, 01:26 AM
Replies: 9
Views: 4,408
Posted By dnusol
Hi Victoria, I guess you could use several...

Hi Victoria, I guess you could use several databases to increase your chances of annotation. What databases have you used? I don't have experience with protists but in general a good start could be...
Forum: Bioinformatics 02-06-2014, 11:45 PM
Replies: 9
Views: 4,408
Posted By dnusol
I think Blast2GO would also be useful

I think Blast2GO would also be useful
Forum: Bioinformatics 02-05-2014, 02:13 AM
Replies: 6
Views: 2,102
Posted By dnusol
Hi there it seems that FreeBayes has not...

Hi there

it seems that FreeBayes has not been published yet. Is this so?

http://arxiv.org/abs/1207.3907


Thanks

Dave
Forum: Bioinformatics 01-27-2014, 01:52 AM
Replies: 2
Views: 1,755
Posted By dnusol
you can also check Blast2GO for assembly...

you can also check Blast2GO for assembly annotation and REVIGO for visualization of GO lists

HTH
Forum: Bioinformatics 01-27-2014, 01:45 AM
Replies: 2
Views: 1,488
Posted By dnusol
Hi RickBioinf, I think the first thing to do...

Hi RickBioinf,

I think the first thing to do could be to check on CLCbio website for publications using CLCbio

http://www.clcbio.com/support/papers/

In addition to this, I am sure CLC has...
Forum: Bioinformatics 01-24-2014, 04:43 AM
Replies: 3
Views: 15,616
Posted By dnusol
Thanks for your input dpryan, it is very helpful....

Thanks for your input dpryan, it is very helpful.
I think I understand the example of a chromosomal inversion. I am trying to interpret the SAM format for such reads.
So does a chimeric alignment...
Forum: Bioinformatics 01-24-2014, 03:21 AM
Replies: 3
Views: 15,616
Posted By dnusol
Not primary vs Supplementary alignment

Hi,

can anyone explain to me the difference (if there is one) between a read having a 0x100 flag (not primary alignment) and a read having a 0x800 flag (supplementary alignment)? How does the...
Forum: Bioinformatics 12-03-2013, 04:48 AM
Replies: 9
Views: 7,235
Posted By dnusol
Hi, we are seeing in IGV some variants being...

Hi,

we are seeing in IGV some variants being called by samtools that seem odd for amplicons, specially at the end of the Miseq reads.
We have also noticed that reads are split across amplicons....
Forum: Bioinformatics 06-17-2013, 03:22 AM
Replies: 6
Views: 5,715
Posted By dnusol
Maybe RNAseq is biased by nature? Check these...

Maybe RNAseq is biased by nature?
Check these other threads

http://seqanswers.com/forums/showthread.php?t=27911
http://seqanswers.com/forums/showthread.php?t=17601...
Forum: Bioinformatics 06-13-2013, 11:57 PM
Replies: 6
Views: 5,715
Posted By dnusol
This link might be useful ...

This link might be useful

http://bioinfo-core.org/index.php/9th_Discussion-28_October_2010
Forum: Bioinformatics 06-11-2013, 01:26 AM
Replies: 1
Views: 1,313
Posted By dnusol
Transcripts missing from cufflinks

Hi, I am moving this thread from the RNA Sequencing group, in case anyone here has some ideas. From my search, this is an issue that comes up every now and then with very few comments. I emailed...
Forum: Bioinformatics 06-05-2013, 07:49 AM
Replies: 6
Views: 4,542
Posted By dnusol
You could try Picard's SortSam. HTH

You could try Picard's SortSam.

HTH
Forum: Bioinformatics 06-04-2013, 03:00 AM
Replies: 0
Views: 922
Posted By dnusol
Annotating INDELs with 1000g

Hi,

Using Samtools I have obtained a .vcf file with some variants, including INDELs. I am trying to compare them to 1000g for frequency, but I am finding difficulties trying to find the INDELs...
Forum: RNA Sequencing 05-30-2013, 12:39 AM
Replies: 3
Views: 3,513
Posted By dnusol
Dear njdickens and all, I am bringing up...

Dear njdickens and all,

I am bringing up this old thread because I am facing a similar issue. I have run a tophat-cufflinks-cuffcompare-cuffdiff workflow on a set of 185k assembled contigs by...
Forum: Bioinformatics 05-23-2013, 08:41 AM
Replies: 15
Views: 6,429
Posted By dnusol
I think this was solved elsewhere ...

I think this was solved elsewhere

http://seqanswers.com/forums/showthread.php?t=16965


HTH
Forum: Bioinformatics 05-22-2013, 01:04 AM
Replies: 1
Views: 1,104
Posted By dnusol
In case it helps anyone, I found this article...

In case it helps anyone, I found this article with one possible solution:

Bioinformatics. 2013 May 8.
Detection of Significantly Differentially Methylated Regions in Targeted Bisulfite Sequencing...
Forum: Bioinformatics 05-15-2013, 01:28 AM
Replies: 1
Views: 1,104
Posted By dnusol
how to compare methylomes

Hi, I am new to bisulfite sequencing and am confronted with an experiment where I would have to compare methylation states for several samples, some of which are paired (i.e. same individual,...
Forum: Bioinformatics 01-16-2013, 06:57 AM
Replies: 7
Views: 3,199
Posted By dnusol
I am not sure, but how about using formatdb...

I am not sure, but how about using formatdb instead of makeblastdb?

HTH

Edit: formatdb is discontinuated but I have used it recently with apparently no errors when running blast 2.26+
Forum: Bioinformatics 11-07-2012, 07:36 AM
Replies: 2
Views: 1,336
Posted By dnusol
dear Sarosh, did you manage to get the per...

dear Sarosh,

did you manage to get the per base ACGT count in any way?

best,

Dave
Forum: Bioinformatics 11-07-2012, 03:22 AM
Replies: 7
Views: 2,952
Posted By dnusol
hi bfantinatti, did you manage to get...

hi bfantinatti,

did you manage to get positions with 0 coverage in your mpileup output?

cheers,

D.
Forum: Bioinformatics 09-25-2012, 08:01 AM
Replies: 12
Views: 6,757
Posted By dnusol
DigiNorm on Paired-end samples

Hi,

how does DigiNorm handle paired-end fastq files? I read in the article that it does not take it into account. But then how to work with the output for de-novo assembly of transcriptome if...
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