Hello everyone,
Currently I am trying to identify novel lncRNAs. I just used cuffCompare and generate several files including .tmap file....
43 results in 0.0032 seconds.
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can I transform .tmap to .gtf/.gff?
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Cuffcompare server issue
Hi,
I am trying to finish a Coursera course that is using the Tuxedo suite including among other platforms, Cuffcompare. I cannot get it... -
Differential expression using TopHat/Cufflinks, analysis by CumeRbund
I am trying to do differential expression analysis for 6 samples with no replicates
The protocol used by me after following several threads... -
Cuffmerge error (GFaSeqGet): subsequence cannot be larger than
Hi all. I am doing some differential expression calculations using the Tuxedo pipeline. I've take all reference files (GTF, reference genome) from ensembl... -
cuffcompare- extract locus information from XLOC/TCONS
I'm trying to look for potentially novel lncRNAs using cuffcompare. My plan was to go through the 'u' class of unknown intergenic transcripts but I'm...Last edited by roniederer; 02-10-2015, 06:09 AM. -
Filter cuffcompare by FPKM
How do I filter out low cuffcompare FPKM values out of by combined.gtf file?
I am trying to use the lncrScan workflow for novel long non-coding... -
Cuffcompare merged.gtf to self not all "="
I have been working on comparing the results of 20 merged.gtf files to see the differences between each pair of files. When doing this work, I used the... -
Advice Needed on Tuxedo Suite
Hi Everyone,
I am working on a project with two groups (A & B) each containing 5 samples. Within each sample I have two RNA-seq FASTQ... -
Cuffcompare to add tss_id to GTF
Hi all,
I am currently trying to run cuffdiff for a DE analysis on RNA seq stranded reads aligned to transcriptome using bowtie2. I first... -
Is my cuffcompare output reasonable?
I've run cuffcompare for the first time and am wondering if my results are reasonable?
Here are the stats:
# Cuffcompare v1.3.0... -
Cuffcompare with a single experiment
I am running RNA-seq analysis on a paired-end deep sequencing data set with no replicates. We are interested in finding novel gene and transcript isoforms... -
Cuffcompare: difference between "nearest_ref" and "oID"
Hello Everyone,
I am a master student new to cufflinks and i am using cuffcompare in order to evaluate an overall analysis on the same... -
Cuffcompare not showing all query transcripts
Hi,
I have 3 reference annotation GTF files and 3 query GTF files which were generated by Tophat-Cufflinks combination.
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Nothing happens after cuffcompare.
Hello all,
With a cuffmerge result (into ./cufflinks_all/merged.gtf), I am trying to cuffcompare it against a reference gtf (../public/publicCuffMergedLncProts/merged.gtf)... -
CuffCompare basic question
Hello,
I was wondering if the reads from the Cuff compare class code J (novel transcript) were also included in the top hat junctions.bed file....
