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Forum: Bioinformatics 08-24-2016, 01:07 PM
Replies: 2
Views: 1,349
Posted By TPH
Hi Melissa, Thank you for the reply. Will give...

Hi Melissa,
Thank you for the reply. Will give a try on Bedtools then.
Best,
Pabodha
Forum: Bioinformatics 07-18-2016, 01:27 PM
Replies: 2
Views: 1,349
Posted By TPH
Question how to find exon combination of a given transcript

Hi,

I have a set of transcript sequences retrieved from cufflinks output through gffread -w and a pool of exon sequences of the gene of interest. Transcripts have unique ids given by cufflinks...
Forum: Literature Watch 03-07-2016, 12:17 PM
Replies: 8
Views: 13,213
Posted By TPH
Hello, I am trying to install GFOLD into the...

Hello,
I am trying to install GFOLD into the Linux cluster I am working in. But I keep getting an error message saying g++: command not found
gsl/1.16 is already installed in the cluster. So I...
Forum: Bioinformatics 03-01-2016, 01:42 PM
Replies: 0
Views: 681
Posted By TPH
Exclamation Is it possible to pull out exon sequences from cuffmerge out?

Hi,
I am interested in studying exon sequences of a particular gene in my cuffmerge output. Is it possible to pull out those sequences using exon IDs and gene ID?
Could anyone please help.
Thank...
Forum: Bioinformatics 02-21-2016, 08:22 PM
Replies: 0
Views: 1,137
Posted By TPH
Question DEXseq input file

Hello!

I am trying to assess expression level of a particular gene and its isoforms in 2 treatment conditions using DEXseq.
I am new to DEXseq and have a question regarding its input file.
I...
Forum: Bioinformatics 02-17-2016, 08:13 AM
Replies: 2
Views: 979
Posted By TPH
Seems like bad luck. I think I'd be able to move...

Seems like bad luck. I think I'd be able to move to linux. Thank you very much.
Forum: Bioinformatics 02-16-2016, 11:28 AM
Replies: 2
Views: 979
Posted By TPH
Question Install pysam for DEXSeq package

Hello,
I am trying to use DEXSeq package to access exon expression of my RNA seq data. Since my tophat2 output is in .bam format I need to install pysam package. But I keep getting following error...
Forum: Bioinformatics 02-03-2016, 08:58 AM
Replies: 6
Views: 3,785
Posted By TPH
Hi, I am getting same kind of an error while...

Hi,
I am getting same kind of an error while trying to execute following command.
csVolcanoMatrix(genes(cuff_data))

Error: geom_vline requires the following missing aesthetics: xintercept

I...
Forum: Bioinformatics 01-28-2016, 01:59 PM
Replies: 10
Views: 1,193
Posted By TPH
Thank you so much.

Thank you so much.
Forum: Bioinformatics 01-28-2016, 12:57 PM
Replies: 10
Views: 1,193
Posted By TPH
yea that's the output I have. So using "cat"...

yea that's the output I have. So using "cat" command for the accepted_hits.bam files would work as same as concatenating starting fastq files. Thank you very much.
Yes, I am using Cuffdiff for the...
Forum: Bioinformatics 01-28-2016, 11:13 AM
Replies: 10
Views: 1,193
Posted By TPH
I work in a cluster. I did the analysis by...

I work in a cluster. I did the analysis by executing tophat command individually to each of the seven files with its paired file without any concatenation. I realized later the way I feed the data in...
Forum: Bioinformatics 01-28-2016, 10:44 AM
Replies: 10
Views: 1,193
Posted By TPH
Thanks again, I saw in a post...

Thanks again, I saw in a post (https://www.biostars.org/p/78456/) it is not recommended to concatenate data but run in parallel instead. Its totally clear how concatenated data can use for the...
Forum: Bioinformatics 01-28-2016, 10:24 AM
Replies: 10
Views: 1,193
Posted By TPH
Thank you very much. really appreciate your help

Thank you very much. really appreciate your help
Forum: Bioinformatics 01-28-2016, 09:09 AM
Replies: 10
Views: 1,193
Posted By TPH
Post Tuxedo suite / Parallel Processing

Hello,
I have a paired-end RNAseq data set for two treatment conditions without any replicates. I want to check isoform variation in a particular gene and gene expression variations in general. Two...
Forum: Bioinformatics 01-21-2016, 12:34 PM
Replies: 0
Views: 876
Posted By TPH
Question cummeRbund error

Hello,

After completing all the analysis steps from Tophat to Cudiff, I am trying to plot the data using CummeRbund. But I get this error message saying "semi-transparency is not supported on this...
Forum: Bioinformatics 01-15-2016, 02:46 PM
Replies: 6
Views: 2,049
Posted By TPH
Hi, Thank you very much for your help. I am...

Hi,
Thank you very much for your help. I am working on a cluster. They have moved index files to another folder location. I Guess that's the reason I was getting those error messages. Now the script...
Forum: Bioinformatics 01-12-2016, 03:55 PM
Replies: 6
Views: 2,049
Posted By TPH
Thank you very much. I'll try doing that.

Thank you very much. I'll try doing that.
Forum: Bioinformatics 01-12-2016, 03:46 PM
Replies: 6
Views: 2,049
Posted By TPH
Hi, Thank you so much for your kind help. ...

Hi,
Thank you so much for your kind help.
Anyway this is the output I get

@SRR057634.1 HWUSI-EAS230-R:1:2:28:1908 length=36
CCCCCCCCCCCCCCCCCCCCCNCCCCCCCCCCCCCC
+SRR057634.1...
Forum: Bioinformatics 01-12-2016, 03:32 PM
Replies: 6
Views: 2,049
Posted By TPH
Question Tophat/Bowtie

Hi, I am self learning tuxedo suite for RNA-seq analysis. I keep getting error messages and some how I can not go forward beyond tophat. I downloaded .gtf file using UCSC ...
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