Hi,
After running velveth. velvetg and oases on the SRP file, the trasncripts file generated is empty.
In previous steps,...
14 results in 0.0022 seconds.
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Velvet+Oases Generating empty transcripts and contigs file
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WORKSHOP: De Novo Transcriptome Analysis
De Novo Transcriptome Analysis
Assembly and Differential Gene Expression in Non-Model Organisms
When? 5 - 7 October... -
using STAR+Cufflinks for transcript assembly turns unstranded RNA-seq to stranded?
I am trying to use STAR+Cufflinks to do a reference based transcript assembly using unstranded RNA-seq data.
As mentioned in the STAR... -
How to extract assembled transcript sequence from RNA-seq data instead of ref genome?
Hi All,
I have a RNA-seq data from a 'subspeices' or 'variety' of grape. Grape genome is available.
I want to get the transcript... -
High level of novel exons/introns in cuffcompare data
Hello, all.
I am new to the forums and the whole of bioinformatics (I've been at it two weeks), but I have done a good deal of reading... -
Cufflinks: Missing assembly of reads
I am working on the zebrafish genome. I took out two regions of the genome hence called good and tricky
good: chr1 44689765 44728408... -
Cufflinks missing transcript assembly in random genomic loci
Dear All,
I am running Cufflinks on RNAseq data from 2 samples. The parameters I have used for both the samples are
--frag-bias-correct... -
Alternative to Cufflinks for transcript assembly and abundance count?
Hi,
I have mapped RNA-seqs with tophat, but cannot run the resulting .bam file through cufflinks because of too large BAM header. Anyone... -
cufflinks question
Hello,
I work with a polyploid species. I would like to use cufflinks to get a better assembly out of my data than I have been able to... -
Hi guys,nice to see you here
hello everyone,
i am a newer from china, focusing on wheat genomics. And now i have trouble in assembling wheat NGS transcriptome data... -
cufflinks not able to assemble transcripts in high read coverage area
Hey Guys
I am using cufflinks for building transcriptome. I am seeing some regions where in-silico model predictions is re-affirmed by... -
n50 value for transcriptome assembly
Hi,
I am doing a Denovo transcriptome assembly using oases. I would like to know about the relation between n50 value obtained from velvet...Last edited by Ramprasad; 10-17-2011, 06:27 AM. -
Map transcripts from de novo assemblier such as trinity back to the genome ?
Hi, could anyone recommend any software or algorithm to map the transcripts generated from de novo assembly algorithm such as trinity back to the reference... -
Using Cufflinks with AB SOLiD Data?
Has anyone tried to use cufflinks to assemble isoforms from SOLiD RNA-Seq data? Now that Bowtie supports colorspace reads, I am trying to take this output...
