Forum: Bioinformatics
11-13-2014, 07:49 AM
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Replies: 34
Views: 10,356
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...
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Forum: Bioinformatics
09-17-2014, 03:34 AM
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Replies: 11
Views: 4,354
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Forum: Bioinformatics
07-23-2014, 01:43 AM
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Replies: 20
Views: 13,813
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Forum: Bioinformatics
07-21-2014, 08:32 AM
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Replies: 1
Views: 1,577
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...
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Forum: Bioinformatics
02-25-2014, 01:26 AM
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Replies: 9
Views: 4,496
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...
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Forum: Bioinformatics
02-06-2014, 11:45 PM
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Replies: 9
Views: 4,496
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Forum: Bioinformatics
02-05-2014, 02:13 AM
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Replies: 6
Views: 2,176
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Forum: Bioinformatics
01-27-2014, 01:52 AM
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Replies: 2
Views: 1,800
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Forum: Bioinformatics
01-27-2014, 01:45 AM
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Replies: 2
Views: 1,518
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...
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Forum: Bioinformatics
01-24-2014, 04:43 AM
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Replies: 3
Views: 16,037
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Forum: Bioinformatics
01-24-2014, 03:21 AM
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Replies: 3
Views: 16,037
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...
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Forum: Bioinformatics
12-03-2013, 04:48 AM
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Replies: 9
Views: 7,303
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....
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Forum: Bioinformatics
06-17-2013, 03:22 AM
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Replies: 6
Views: 5,891
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Forum: Bioinformatics
06-13-2013, 11:57 PM
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Replies: 6
Views: 5,891
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Forum: Bioinformatics
06-11-2013, 01:26 AM
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Replies: 1
Views: 1,337
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...
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Forum: Bioinformatics
06-05-2013, 07:49 AM
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Replies: 6
Views: 4,646
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Forum: Bioinformatics
06-04-2013, 03:00 AM
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Replies: 0
Views: 940
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...
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Forum: RNA Sequencing
05-30-2013, 12:39 AM
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Replies: 3
Views: 3,594
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...
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Forum: Bioinformatics
05-23-2013, 08:41 AM
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Replies: 15
Views: 6,499
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Forum: Bioinformatics
05-22-2013, 01:04 AM
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Replies: 1
Views: 1,130
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...
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Forum: Bioinformatics
05-15-2013, 01:28 AM
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Replies: 1
Views: 1,130
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,...
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Forum: Bioinformatics
01-16-2013, 06:57 AM
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Replies: 7
Views: 3,311
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+
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Forum: Bioinformatics
11-07-2012, 07:36 AM
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Replies: 2
Views: 1,395
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Forum: Bioinformatics
11-07-2012, 03:22 AM
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Replies: 7
Views: 3,015
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Forum: Bioinformatics
09-25-2012, 08:01 AM
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Replies: 12
Views: 6,867
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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