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• Very long run time in Freebayes Galaxy
  Hi! I am doing the course project on Coursera in Genomic Data science that requires mapping three...
• Tophat taking for a long time
  I am running Cufflinks of a couple of dozens of RNAseq Bam files from using mm9 as a reference. F...
• Help with genomics courese question
  Hello Biostar members, I am currently taking a course and we have some homework in which we need ...
• Long wait times
  Hi, I understand there was a clustering issue this weekend and it has been resolved. I re-entere...
• Job Running Speed Is Really Slow
  Dear Galaxy team, I found glalaxy (website) is running really slow today. I just did some text m...
• Galaxy job taking bit too long for uploading and processing datasets
  I am trying to upload several ChIP-seq sequencing results from my own computer through ftp. Most ...
• Bowtie2/FreeBayes/mpileup variant detection on NGS of PCR amplicons around Cas9/CRISPR indels
  Hey threre, I have an MiSeq experiment using 24 indices where in each index I was sequencing 3 P...
• Fastq.gz files taking a long time to upload
  Hello, I am trying to upload two files, both of which are about 2.4 GB and in fastq.gz format. I...
• Convert To Bigwig
   Hello I have been trying to convert a number of BedGraph files to BigWig for several weeks now....
• upload 1 BAM file (2.6G) in queue since 4 hours
  Hello, I am trying to upload one single BAM file as a test, through ftp. I don't have other job r...
• Snp Calling Problems
  Dear all, I have been looking for an answer to my problem in all the Galaxy Support resources bu...
• Problems with the Upload function at https://usegalaxy.org -- Workaround included, follow for updates
  Hello I am new in Galaxy (usegalaxy.org). I am trying to load fastq.gz files in galaxy from FTP,...
• Trim Galore run time issue
  Hello, I am following the tutorial for NGS Quolity Control. I reached the step where the Trim Gal...
• Slow BAM uploads
  Hi, I am trying to upload BAM files from an external hard drive on to galaxy, but it is very slo...
• Downloading "Accepted Hits" (BAM) files is EXTREMELY Slow at the Moment
  I have uploaded 7 FastQ datasets into Galaxy and used TopHat to align these datasets against a ge...
• Fastq upload times
  Hey there I am trying to upload a fastq fiel since last night is less than 1Gb and still in queu,...
• Job not running
  My jobs are taking a very long time to run, it takes at least 15min for 1 job to run. I'm not too...
• Unable to view .bam files in Integrated genome browser (IGB)
  Hello, I am trying to view Bowtie2 mapped .bam file in IGB. But it is taking a lot of time to up...
• megablast to long
  Hi, I am running a megablast and is take too long, I launched in august 10 and is still runnning....
• Chimera.uchime issue in mothur pipeline
  Is there a way that I can see the logfile in real time? I want to check if the uchime step is run...
• Tophat taking too much time
  Is this a server error or data size overload?? Tophat is still running since long time. I got res...
• Estimating Galaxy On The Cloud Needs For Rnaseq
  Questions: I have been running sets of data for cufflinks/cuffdiff analysis on Galaxy online--I ...
• Running FreeBayes to a collection of BAM files individually
  Actually, the FreeBayes variant calling tool generates one VCF file for "all" BAM files selected ...