How many loci can expect from cufflinks output

Hai every one

I did a transcriptome assembly with tophat and followed by cufflinks for Pseudomonas aeruginosa. After processing gtf file got 38 loci, Is it a good number? How many loci can expect from cufflinks output for bacterial species?

genome rna-seq sequencing tophat

• 1,743 views • link

written 10.4 years ago by Eva_Maria

Really, I don't know, but these guys in this paper are seeing around 3000 TSS

• 0 views • link

written 10.4 years ago by Fabio Marroni

0 answers

No answers yet.

More posts like this

Processed loci from Cufflinks
written 6.5 years ago by Munmun •

I'm running Cufflinks from the output of TopHat as well from the output of HISAT2 and Bowtie2-align. The number of processed loci are highly variable …
How to fetch sequences from Proteinortho5 output containing all test species and no duplication in…
written 7.6 years ago by saadleeshehreen

Hi, I want to construct a phylogenic tree on 100 *Pseudomonas aeruginosa* genomes. Before constructing the tree, I want to first cluster those genomes on …
to much time for using cufflinks
written 9.2 years ago by hasani.iut6

Hi all, I want to run cufflinks pipeline explained in [it's site][1]. I have used the paired-end sample from the [Illumina body map][2] project with …
Empty Cuffdiif Output except Gene Differential expression testing
written 9.3 years ago by benjyrolls

Hello I am running a Cuffdiff on two separate conditions of a file. all outputs seem to be empty except the gene differential expression output …
cufflink and cuffmerge error
written 10.2 years ago by santosh.bicnehu •

Hi everyone, I am getting an error while running cuffmerge with the follwing options: cuffmerge -g genes.gtf -s genome.fa -p 2 assembled_tc.txt this is the …
cufflink and cuffmerge error
written 10.2 years ago by santosh.bicnehu •

Hi everyone, I am getting an error while running cuffmerge with the follwing options: **cuffmerge -g genes.gtf -s genome.fa -p 2 assembled_tc.txt** this is the …
Cufflinks displaying "WARNING: Multi-Hit not found"
written 10.2 years ago by Antonio Camargo

I'm running Cufflinks (2.2.1) on a set of RNA-seq alignments that I did with STAR. I'm using these options: /home/user1/Data/Softwares/cufflinks-2.2.1/cufflinks -p 6 -u -o ./Cufflinks/ERR036348_pass-2 …
Can I use own transcriptome without GTF file?
written 11.1 years ago by jhkim1972 •

I am a novice of RNA-Seq analysis. For differentially expressed genes analysis, I am trying to run bowtie/tophat and cufflinks pipeline with own transcriptome as …
Gene expression level with RNA-seq
written 11.3 years ago by bharata1803

Hello all, I want to ask a basic question because this is the first time I try RNA-seq analysis. My original task is basically to …
Tune Star Parameters For Transcriptome Assembly (Cufflinks)
written 13.2 years ago by Nicolas Rosewick

<p>Hi,</p> <p>Lately, I was playing a little bit with STAR and cufflinks to perform transcriptome assembly. I have a gtf file but it is not …