Forum: Bioinformatics
11-30-2017, 09:14 AM
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Replies: 1
Views: 2,601
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Forum: Bioinformatics
01-22-2014, 12:02 AM
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Replies: 13
Views: 3,390
vfs running
hi everyone
(if anyone is there!!!)
I run the vfs example 1.VFS.sys.check.pl and got nothing. this is the report after i submitted the job:
Make sure BWA is installed and is available in PATH...
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Forum: Bioinformatics
01-21-2014, 02:32 AM
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Replies: 13
Views: 3,390
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Forum: Bioinformatics
01-21-2014, 02:31 AM
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Replies: 13
Views: 3,390
Hello everyone,
quick question about vfs: to...
Hello everyone,
quick question about vfs: to save my viral genome of interest, is is enough to use the fasta file from NCBI website (http://www.ncbi.nlm.nih.gov/nuccore/4927719?report=fasta) and...
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Forum: Bioinformatics
01-16-2014, 11:16 PM
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Replies: 13
Views: 3,390
Thanks Marco,
I have run 1.VFS.sys.check.pl...
Thanks Marco,
I have run 1.VFS.sys.check.pl but where can I see the output?
No error came up, so shall I assume everything is correctly installed with correct dependencies?
Thanks very much, ...
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Forum: Bioinformatics
01-16-2014, 07:09 AM
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Replies: 13
Views: 3,390
hi everyone,
hope I'm in the right place!
...
hi everyone,
hope I'm in the right place!
I need to use vfs to detect fusions in my sequenced samples.
I am a very beginner on unix, thus im havng problems to get started:
I have downloaded...
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Forum: RNA Sequencing
12-02-2013, 03:57 PM
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Replies: 6
Views: 3,327
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Forum: Bioinformatics
11-15-2013, 11:28 AM
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Replies: 5
Views: 4,411
Hello guys,
if anyone knows, could you please...
Hello guys,
if anyone knows, could you please tell me why is this happening:
i ran cufflinks on galaxy with default parameters and had satisfactory results.
I then ran the same samples with...
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Forum: Bioinformatics
10-30-2013, 12:19 AM
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Replies: 5
Views: 4,906
hi all,
can anyone tell em how to fix this?
...
hi all,
can anyone tell em how to fix this?
head(features(myGene))
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function "features", for signature...
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Forum: RNA Sequencing
10-24-2013, 04:37 AM
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Replies: 61
Views: 36,635
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Forum: RNA Sequencing
10-18-2013, 12:28 AM
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Replies: 61
Views: 36,635
Dear all,
any suggestion about this issue I...
Dear all,
any suggestion about this issue I have?
I run the following commands:
> library (cummeRbund)
Loading required package: RSQLite
Loading required package: DBI
Loading required...
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Forum: Bioinformatics
10-18-2013, 12:26 AM
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Replies: 2
Views: 1,317
Dear all,
any suggestion about this issue I...
Dear all,
any suggestion about this issue I have?
I run the following commands:
> library (cummeRbund)
Loading required package: RSQLite
Loading required package: DBI
Loading required...
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Forum: Bioinformatics
10-16-2013, 02:04 AM
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Replies: 15
Views: 16,689
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Forum: Bioinformatics
10-16-2013, 01:41 AM
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Replies: 15
Views: 16,689
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Forum: Bioinformatics
10-16-2013, 01:41 AM
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Replies: 15
Views: 16,689
Hi,
I have human cervical samples. No...
Hi,
I have human cervical samples. No replicates. this one i posted is one of the samples I have compared with the negative sample...
i'm struggling writing down commands...! I need to create a...
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Forum: Bioinformatics
10-15-2013, 06:12 AM
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Replies: 15
Views: 16,689
hi,
can anyone help me out with this?
>...
hi,
can anyone help me out with this?
> library(cummeRbund)
Loading required package: RSQLite
Loading required package: DBI
Loading required package: ggplot2
Loading required package: reshape2...
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Forum: Bioinformatics
10-18-2012, 01:50 AM
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Replies: 16
Views: 13,585
Hi Artur,
yes, that makes sense. Thus I shall...
Hi Artur,
yes, that makes sense. Thus I shall not take in consideration the p/q values and their consequent significance.
I did follow the tophat/cufflinks/cuffcompare/cuffdiff pipeline, but I...
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Forum: Bioinformatics
10-17-2012, 01:10 PM
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Replies: 5
Views: 5,357
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Forum: Bioinformatics
10-17-2012, 01:07 PM
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Replies: 6
Views: 11,828
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Forum: Bioinformatics
10-17-2012, 01:03 PM
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Replies: 3
Views: 21,040
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Forum: Bioinformatics
10-17-2012, 01:02 PM
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Replies: 3
Views: 21,040
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Forum: Bioinformatics
10-17-2012, 01:00 PM
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Replies: 16
Views: 13,585
Calculating p-values from FPKM and more...
Hi Artur,
I read with interest your last conversation abt the statistic to be used.
I am new to this filed and very new to the statistic field, thus I am completely lost!
here my issue: I have...
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Forum: Bioinformatics
10-17-2012, 05:17 AM
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Replies: 17
Views: 12,746
Hi mbblack,
thanks. I think I understood your...
Hi mbblack,
thanks. I think I understood your point of view. I shall look at the data by simply looking at the fold change and ignoring the fpkm values equal to zero from both samples.
Thanks a...
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Forum: Bioinformatics
10-17-2012, 02:20 AM
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Replies: 17
Views: 12,746
Hi,
I was going through the cuffdiff manual...
Hi,
I was going through the cuffdiff manual where it says "If there are no replicates, the variance is measured across the conditions under the assumption that most transcripts are not...
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Forum: Bioinformatics
10-16-2012, 08:57 AM
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Replies: 17
Views: 12,746
thanks mbblack,
one thing i don't get...so you...
thanks mbblack,
one thing i don't get...so you suggest to rank by fpkm value, exclude those where this is=0 and then rank the rest by fold change? so this means that we do not consider whether they...
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