Hey everybody,
I am a newbie in coding in Bioinformatic and I have a question.
Using a HPC I perform a quality control and...
13 results in 0.0021 seconds.
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KEGG with pathview using CuffDiff data
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Finding isoform sequences for Differentially spliced genes
I've performed RNA-Seq analysis for A. thaliana using the TopHat/Cufflinks pipeline for 2 conditions. How can I extract the sequences of all isoforms... -
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... -
What do I do with output files from tophat/cufflinks
Hi I am a beginner with RNA-sequencing and I used tophat to align RNA-seq reads from geuvadis to hg19 from UCSC. In tophat, I provided the reference transcript... -
how will manipulating low quality base pairs of reads affect TopHat and Cufflinks?
Hi all,
I am working with a paired-end Illumina 2*250bp reads (16S rRNA). The quality is extremely low (i.e. with quality filtering only... -
cuffDiff "cannot open reference GTF file"
I am running a series of Tuxedo pipelines and have run into the following error message a number of times in CuffDiff "cannot open reference GTF... -
Strand-specific Expression analysis in Cufflinks
I'm trying to use TopHat and Cufflinks mainly for differential gene expression analysis according to the protocol by Trapnell et al. (Differential gene... -
cufflinks configuration
Hi,
I'm trying to define the best options configuration of Cufflinks. In order to estimate only known transcripts, is my command-line right or... -
Cuffdiff with and without Quantile Normalization
Hello experts,
I am following the recently published Nature Protocol guideline for analyzing my RNA-seq runs using tophat-cufflink-cuffmerge-cuffdiff... -
cufflinks : difference in --GTF and --GTF-guide result
Hi all,
I've run transcriptome data analysis on bacteria samples. However, I'm puzzle on expression result differences between... -
Is it normal for cufflinks produce different results in multiple run
I have running cufflink on 0.9M paired end sam data of human RNA and gtf annotations.
The GTF annotations were constructed based on the... -
Cufflink's handling of reads
I am using Cufflinks to analyze RNAseq data and comparing different samples.
I run the programs with the following options:
...Code:cufflinks --num-threads
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Cufflinks
Hi,
Has anybody tried the new cufflinks package?
http://cufflinks.cbcb.umd.edu/
I tried using it on my .gtf file...
