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Search: Posts Made By: kasutubh
Forum: Bioinformatics 02-14-2013, 02:20 PM
Replies: 3
Views: 1,670
Posted By kasutubh
Hi Bruce, I'm still unable to understand why it...

Hi Bruce,
I'm still unable to understand why it can't find the function. I tried to update all the bioconductor packages..but the error remains.
Forum: Bioinformatics 02-14-2013, 09:33 AM
Replies: 3
Views: 1,670
Posted By kasutubh
Could not find function 'estimateDispersion' error

Hi..
I'm running DESeq (2.11) on R (2.25.2) on windows 7 . I'm getting following error,
Error: could not find function "estimateDispersion"
Do I need to update anything or what am I doing wrong...
Forum: Bioinformatics 02-13-2013, 03:05 PM
Replies: 13
Views: 6,306
Posted By kasutubh
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...
Forum: Bioinformatics 08-07-2012, 12:00 PM
Replies: 2
Views: 1,666
Posted By kasutubh
Hi Wolfgang, Thanks for your reply. It works...

Hi Wolfgang,

Thanks for your reply. It works now..

Best wishes,

Kaustubh
Forum: Bioinformatics 08-06-2012, 05:01 PM
Replies: 2
Views: 1,666
Posted By kasutubh
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...
Forum: Bioinformatics 08-06-2012, 03:37 PM
Replies: 8
Views: 9,738
Posted By kasutubh
Hi Simon, I tried the latest version and also...

Hi Simon,
I tried the latest version and also added the attributes..it works now.
Thanks a lot..
Best,
Forum: Bioinformatics 08-02-2012, 01:26 PM
Replies: 8
Views: 9,738
Posted By kasutubh
Hi Simon, Thanks a lot for the reply. I'll try...

Hi Simon,
Thanks a lot for the reply. I'll try the latest version!
Best,
Forum: Bioinformatics 08-01-2012, 08:24 PM
Replies: 8
Views: 9,738
Posted By kasutubh
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...
Forum: Bioinformatics 04-03-2012, 06:29 PM
Replies: 1
Views: 1,224
Posted By kasutubh
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...
Forum: Bioinformatics 03-31-2012, 01:46 PM
Replies: 1
Views: 1,224
Posted By kasutubh
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...
Forum: Bioinformatics 03-20-2012, 07:57 PM
Replies: 1
Views: 2,403
Posted By kasutubh
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...
Forum: Bioinformatics 03-19-2012, 05:31 PM
Replies: 4
Views: 1,883
Posted By kasutubh
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...
Forum: Bioinformatics 03-19-2012, 05:26 PM
Replies: 0
Views: 1,391
Posted By kasutubh
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....
Forum: Bioinformatics 09-28-2011, 11:17 AM
Replies: 2
Views: 4,088
Posted By kasutubh
Thanks biznatch!

Thanks biznatch!
Forum: Bioinformatics 09-27-2011, 10:47 PM
Replies: 2
Views: 4,088
Posted By kasutubh
Unhappy 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...
Forum: Bioinformatics 09-26-2011, 05:48 PM
Replies: 3
Views: 3,344
Posted By kasutubh
Thank you guys..It worked!

Thank you guys..It worked!
Forum: Bioinformatics 09-26-2011, 12:36 PM
Replies: 3
Views: 3,344
Posted By kasutubh
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...
Forum: Bioinformatics 09-23-2011, 01:11 PM
Replies: 1
Views: 7,986
Posted By kasutubh
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?...
Forum: Bioinformatics 11-25-2010, 01:29 AM
Replies: 3
Views: 2,814
Posted By kasutubh
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...
Forum: SOLiD 05-07-2010, 02:39 AM
Replies: 12
Views: 3,819
Posted By kasutubh
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...
Forum: SOLiD 05-06-2010, 11:37 PM
Replies: 12
Views: 3,819
Posted By kasutubh
Conversion of colourspace into basespace format.

Hello Everyone,

Sorry if this is a re-post..but is there any way to convert SOLiD .bam files data into basespace format. We are trying to use IMAGE algorithm...
Forum: Bioinformatics 05-06-2010, 04:02 AM
Replies: 1
Views: 2,775
Posted By kasutubh
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...
Forum: Bioinformatics 03-11-2010, 12:07 PM
Replies: 7
Views: 2,958
Posted By kasutubh
Thank you 'Ih3'! I've to align 7 individual BACs...

Thank you 'Ih3'! I've to align 7 individual BACs to ~1.2 Mb reference region! I shall try out bwasw. where can I download it?
Forum: Bioinformatics 03-11-2010, 10:06 AM
Replies: 7
Views: 2,958
Posted By kasutubh
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,...
Forum: Bioinformatics 03-09-2010, 10:12 AM
Replies: 7
Views: 2,958
Posted By kasutubh
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....
Showing results 1 to 25 of 25

 


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