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Forum: RNA Sequencing 02-24-2014, 04:06 AM
Replies: 2
Views: 2,318
Posted By mehtaaditya
Thanks....

Thanks....
Forum: RNA Sequencing 05-08-2013, 09:44 AM
Replies: 0
Views: 1,176
Posted By mehtaaditya
Alternative Splice Transcript finding in RNA Seq Study

Hi Every one
I m new in RNA seq study. I m using Tophat and cufflink pipeline for referenced based RNA seq study and differential gene expression. now i want to extract or get alternative splice...
Forum: RNA Sequencing 05-08-2013, 09:30 AM
Replies: 4
Views: 2,793
Posted By mehtaaditya
Thanks....... its works..

Thanks....... its works..
Forum: RNA Sequencing 04-14-2013, 11:07 PM
Replies: 4
Views: 2,793
Posted By mehtaaditya
Tophat Exon -intron coverage

Hi everyone
i mapped my high quality reads on my reference genome using Tophat 2.0.7 ver. Now i want to know how many reads fall (mapped) in my exon and intron regions. and how many reads fall in...
Forum: Bioinformatics 03-19-2013, 09:53 AM
Replies: 0
Views: 1,430
Posted By mehtaaditya
how to run tophat without gtf file and annotate the gene

Hi everyone..
i m working on RNA seq data. i dont have ref genome for my RNA seq data. i have CDS as reference genome file for my referenced. i want to run tophat on the same. how can i run tophat...
Forum: RNA Sequencing 03-18-2013, 11:23 PM
Replies: 2
Views: 2,318
Posted By mehtaaditya
extract gene/transcript sequence from ttophat/cufflink/cuffdiff output

Hi every one
i work on RNA seq data. i used Tophat/cufflink pipeline to study referenced based RNA seq data analysis. after run all the step tophat, cufflink, and last cuffdiff for differential...
Forum: RNA Sequencing 03-13-2013, 09:41 AM
Replies: 2
Views: 4,240
Posted By mehtaaditya
Thanks for your guidance. but how i know presence...

Thanks for your guidance. but how i know presence of trnascript/gene in my transcriptome data?? how to extract gene length from a GFF or even GenBank file? BEDTools does it but I have duplicated...
Forum: RNA Sequencing 03-12-2013, 10:06 AM
Replies: 2
Views: 4,240
Posted By mehtaaditya
calculating Your Transcriptome coverage.. in RNA seq data

Hi every one can anybody tell me
after performing mapping based approach for RNA seq data with tophat-cufflink pipeline i mapped my reads to reference genome and gff file for annotation. then how...
Forum: RNA Sequencing 03-12-2013, 09:39 AM
Replies: 15
Views: 10,076
Posted By mehtaaditya
Tophat-accepted_hits.bam file shows more read with samtools flagstat

Hi i m using tophat-cufflink pipeline for RNA seq data analysis. i have ~26 million high quality paired end reads each pair 1 and pair2. i mapped it on reference genome with tophat and output file...
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