[galaxy-user] primer contamination, miranalyzer

Hi Galaxy, Ive got 2 problems for you; 1) Ive got microRNA Illumina NGS data that I want to analyse, I put it through fastQC on galaxy and it showed that 71% of the reads in one overrepresented sequence; Sequence

Re: [galaxy-user] primer contamination, miranalyzer

Hello Rosie, Pls see below On 11/12/12 4:00 AM, Rosie Griffiths wrote: Hi Galaxy, Ive got 2 problems for you; 1) Ive got microRNA Illumina NGS data that I want to analyse, I put it through fastQC on galaxy and it showed that 71% of the reads in one overrepresented sequence; Sequence

[galaxy-user] cuffdiff

Hi, I got confused while trying to perform Cuffdiff for my RNA sequencing analysis. So I have five different samples which were sequenced. I used tophat to create the bam files and cufflink to create the assembled trancripts. Then I uded Cuffmerge to merge them in one file and then I wanted to

Re: [galaxy-user] Trouble Installing Galaxy on Cluster

So I ended up moving these lines: export DRMAA_LIBRARY_PATH=/sge/current/lib/lx-amd64/libdrmaa.so export TEMP=/scratch/galaxy source /usr/local/galaxy/galaxy_python/bin/activate from galaxy.fedora-init to the galaxy user's .bashrc file. (/home/galaxy/.bashrc) It seems to be working, I see the

Re: [galaxy-user] cuffdiff

Use the replicates option (yes, a bit of a misnomer) and put each Tophat run in its own group. This will produce a tabular file with FPKM for each group/run. Best, J. On Nov 12, 2012, at 10:05 AM, Vevis, Christis wrote: Hi, I got confused while trying to perform Cuffdiff for my RNA

[galaxy-user] Warning message

I'm having issues with the FASTQ_Groomer. What I have done it first I downloaded an SRA file created by an Ion torrent sequencer from the NCBI site. Then used the fastq-dump app from the NCBI site to covert the .sra file to .fastq file. When I uploaded the data into galaxy it recognized it as a