Forum: Bioinformatics
02-14-2013, 02:20 PM
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Replies: 3
Views: 1,707
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Forum: Bioinformatics
02-14-2013, 09:33 AM
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Replies: 3
Views: 1,707
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Forum: Bioinformatics
02-13-2013, 03:05 PM
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Replies: 13
Views: 6,423
Hi..
I'm running DESeq (2.11) on R (2.25.2) on...
Hi..
I'm running DESeq (2.11) on R (2.25.2) on windows platform. I'm getting same error as chrisbala
Error: could not find function "estimateDispersion"
Do I need to update anything or what am I...
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Forum: Bioinformatics
08-07-2012, 12:00 PM
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Replies: 2
Views: 1,697
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Forum: Bioinformatics
08-06-2012, 05:01 PM
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Replies: 2
Views: 1,697
DESeq data analysis
Hi everyone,
I want to use DESeq for rna-seq analysis. I was trying to work out with the trial data when I ran into problem. I wanted to go for DE after estimating the dispersion with the...
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Forum: Bioinformatics
08-06-2012, 03:37 PM
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Replies: 8
Views: 9,910
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Forum: Bioinformatics
08-02-2012, 01:26 PM
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Replies: 8
Views: 9,910
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Forum: Bioinformatics
08-01-2012, 08:24 PM
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Replies: 8
Views: 9,910
Output of HTseq-count?
Hi Everyone,
I'm trying my hands at HTseq-count and was able to run it on our university cluster. We're using version htseq/0.4.6p1. My input command was
htseq-count --stranded=no -o samout q1.sam...
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Forum: Bioinformatics
04-03-2012, 06:29 PM
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Replies: 1
Views: 1,258
Using version 1.3 of cufflinks solved the q>1...
Using version 1.3 of cufflinks solved the q>1 problem..but I also ended up having far less number of significant genes than the old data set now. Has anyone else encountered such a thing? Can use of...
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Forum: Bioinformatics
03-31-2012, 01:46 PM
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Replies: 1
Views: 1,258
q>1 in cuffdiff output
Hi,
I know this question has already been asked (http://seqanswers.com/forums/showthread.php?t=13764z)..but I'm very new to these things and didn't follow the R script..could anyone please break...
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Forum: Bioinformatics
03-20-2012, 07:57 PM
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Replies: 1
Views: 2,447
cuffdiff output
Hi everyone,
I want to analyze data using cummeRbund but I'm having problem with cuffdiff output. I don't get any entries in the gene_id and gene columns in the output files of cuffdiff. Also all...
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Forum: Bioinformatics
03-19-2012, 05:31 PM
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Replies: 4
Views: 1,926
Hi Deepak,
I don't quite understand what you...
Hi Deepak,
I don't quite understand what you need to do. Can you be a bit more clear? If you need to get a combined cufflinks result what you can do is the following,
cufflinks -o output -G...
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Forum: Bioinformatics
03-19-2012, 05:26 PM
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Replies: 0
Views: 1,430
Blank gene_id and gene rows
Hello everyone,
So this is how it goes..I run cuffdiff and end up with all the output files. Only the files with the isoform heading give data..while all the others (genes,tsp,cds) are blank....
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Forum: Bioinformatics
09-28-2011, 11:17 AM
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Replies: 2
Views: 4,157
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Forum: Bioinformatics
09-27-2011, 10:47 PM
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Replies: 2
Views: 4,157
Bowtie .sam and .map output difference?
Hello everyone,
I'm trying to map RNAseq reads to the known genome and my search resulted in 2 commands giving different output. Both are supposedly alignments to the reference file but one is a...
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Forum: Bioinformatics
09-26-2011, 05:48 PM
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Replies: 3
Views: 3,409
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Forum: Bioinformatics
09-26-2011, 12:36 PM
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Replies: 3
Views: 3,409
Bowtie installation
Hi everyone,
I need to install bowtie on my University cluster and I downloaded the linux version of bowtie. (bowtie-0.12.7-linux-x86_64.zip). When I try to copy this to the cluster, I get...
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Forum: Bioinformatics
09-23-2011, 01:11 PM
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Replies: 1
Views: 8,050
Tophat command for single end reads
Hi Everyone,
I'm trying to run tophat on single end illumina reads..but end up getting error message telling me to input the distance between the 2 reads (r). Has anyone run tophat on single runs?...
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Forum: Bioinformatics
11-25-2010, 01:29 AM
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Replies: 3
Views: 2,852
How to merge individual contigs
Hi Everyone,
I would really be thankful if anyone is able to tell me solution to the following,
1. I have sequences some BAC clones and have generated contigs. It turns out that 2 BAC's...
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Forum: SOLiD
05-07-2010, 02:39 AM
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Replies: 12
Views: 3,880
These files were sent to me by the ABI guys. We...
These files were sent to me by the ABI guys. We had asked them to align the sequences to a reference. As a output they have sent these files. What is the raw data format of SOLiD? I need files in the...
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Forum: SOLiD
05-06-2010, 11:37 PM
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Replies: 12
Views: 3,880
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Forum: Bioinformatics
05-06-2010, 04:02 AM
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Replies: 1
Views: 2,808
Use of IMAGE for gap filling using SOLiD runs.
Hello everyone,
We are trying to close gaps between our contigs generated by different sequencing technologies (sanger and 454). In parallel, we also have the SOLiD data for the same and now are...
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Forum: Bioinformatics
03-11-2010, 12:07 PM
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Replies: 7
Views: 3,027
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Forum: Bioinformatics
03-11-2010, 10:06 AM
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Replies: 7
Views: 3,027
Thank you for suggestions-next problem!
Hello again and thank you for your suggestions! I shall try to use them and come up with something. Meanwhile I am facing problems with the installation of Mosaik. I have a XP-Home edition system,...
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Forum: Bioinformatics
03-09-2010, 10:12 AM
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Replies: 7
Views: 3,027
Aligning contigs w.rt reference sequence
Hello everyone,
I am posting a very basic question. I am sorry if this is a repetition..but please give me an answer. We have sequenced some BAC clones and are now in the process of aligning them....
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