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• Cufflinks not working from last 4-5 days
  I am using Galaxy for my RNA seq analysis. I put the cufflinks analysis on BAM files last week. T...
• Bias correction in cufflinks
  I was running a pipeline for DEG analysis of my Arabidopsis RNASeq data, In cufflinks I came acro...
• Cufflinks not activating
  For the past 3 days, Cufflinks has not been working. Everytime I submit a Bam RNA-seq file for a...
• Cufflinks Error In Galaxy
  Hi galaxy dev team: I just installed galaxy on my ubuntu box and tried to do RNA-seq analysis ...
• Cufflinks and inner mean distance
  Greetings, I am attempting to use Cufflinks on alignments produced by running Tophat on some pa...
• Walltime Exceeded
  Dear all, My Cufflinks jobs keep getting killed due to the walltime limit. Is there a way to fix...
• Graduate student learning to do RNAseq analysis
  Hi, I am trying to do RNAseq analysis using Galaxy. I have tophat files which i used to run the c...
• Locally cached sequence not detected from DBkey in cuffmerge when using mm10
  Hi, I'm running a cufflinks pipeline on the public server, and I'm having trouble using the loca...
• Cuffmerge Error
  Hello, The problem is most likely with the SAM files and sorting. Please see: "Why won't my SAM ...
• Processes queing at galaxy
  Hello, I am performing the RNA -seq analysis using my sample on galaxy but the workflow is not ge...
• Cufflinks 0.0.7 and CummeRbound
  Hi All,   Has anyone had any experience with running R package CummeRbound with cufflinks veris...
• number of threads for cufflinks transcript assembly
  Hello everyone I'm using cufflinks to build a transcript.gtf file on ubuntu server. i used this c...
• cufflinks not running
  I am trying to upload my data for cufflinks at usegalaxy,but its not runnng.kindly help
• Cufflinks analysis remains in que without running
  Hi Team, Loving Galaxy! When I run my data, I use the same protocol for most all datasets. Howev...
• RNA Analysis cufflinks
  How long does cufflinks usually take to run on RNA analysis? I had it running for about an hour a...
• Rna-Sea analysis and cufflinks
  Hello, I am using the following pipeline to analyze my RNA-Seq data to detect differences in gen...
• Query for inputting Hisat2 BAM with dataset collections for Stringtie analysis
  Hi, I have data set collections ( 3 biological replicates) that I could run on HiSAT2 and I have...
• How to include ensembl Human annotation FASTA files in Galaxy for cufflinks bias correction
  Hi everyone! I am working on an RNAseq project and have successfully run cufflinks using the Ens...
• Blank Cufflinks output
  Hi! I am conducting an RNA-seq analysis with Saccharomyces cerevisiae-derived data. In my workfl...
• Cufflinks Assigning separate Cuff I.D. to gene that falls within location of known gene
  Hi, I am following the workflow for differential expression analysis using cuffdiff on galaxy as...
• RNA-seq analysis- HiSat2 and Cufflinks
  Hello, I am new with RNA-seq data analysis. I am using Cygwin software in order to create a Linu...
• cufflinks splicing analysis drosophila - 'notest' in output
  Hi everyone, I'm attempting to use cufflinks to examine alternative splicing in my RNAseq data f...
• How to add reference annotation in cufflinks
  how to add reference annotation in cufflink ? I am trying to put my Hisat2 output file in cufflin...