[galaxy-user] How to calculate GC content of transcripts only including exons from a GTF file

Hi everyone, I want to calculate GC content of transcripts in the gtf file like this: chr1 Cufflinks transcript 3 22 1000 + . gene_id CUFF.23955; transcript_id CUFF.23955.1; chr1 Cufflinks exon 3 10 1000 + . gene_id CUFF.23955; transcript_id CUFF.23955.1; exon_number 1; chr1 Cufflinks exon

[galaxy-user] FASTQ joiner

Hi all, Has anyone used FASTQ joiner with a file containing multi-mapped reads? I'm pretty sure i have reads mapped to several locations and i don't know what this tool does with it? will it locate the right map according to the paired read? will it use the first read location and ignore the rest

[galaxy-user] extension of read length

Dear all, I am working on an MNAse-Seq experiment with 50bp single end reads. To identify nucleosome positions, I read that one needs to extend the single reads to approximately the length of nucleosome protected DNA, being approximately 150bp. Is there a way in Galaxy to extend 50bp reads

[galaxy-user] cannot download data to Galaxy

Hello, My connection with Galaxy online shutoff last night while I was transferring data to it. When I tried to connect again with Fetch this morning I was not allowed and a message like Sorry the maximum number of clients for this user are already connected. I have had what appears to be the

Re: [galaxy-user] error message from Filezilla

On Sep 11, 2013, at 7:48 AM, Amit Pande wrote: Hi, I am getting the following error from the server : Command:USER genebus...@googlemail.com Response:331 Password required for genebus...@googlemail.com Command:PASS *** Response:530 Sorry, the maximum number of

Re: [galaxy-user] cannot download data to Galaxy

On Sep 11, 2013, at 9:56 AM, Elwood Linney wrote: Hello, My connection with Galaxy online shutoff last night while I was transferring data to it. When I tried to connect again with Fetch this morning I was not allowed and a message like Sorry the maximum number of clients for this user

Re: [galaxy-user] FASTQ joiner

Lilach: This tool works on unaligned reads in fastq format before they are mapped. It is useful for merging mates together into a single read for QC processing, filtering, and trimming. Thanks! anton On Wed, Sep 11, 2013 at 4:34 AM, lilach noy lilach...@gmail.com wrote: Hi all, Has anyone

[galaxy-user] (no subject)

Hello, I am fairly new to galaxy and I am trying to use bowtie2 to map my reads against a custom genome (specifically a ribosomal RNA fasta file). I have formatted the file as suggested in the Galaxywiki ect and I am still getting the following message: Job output not returned by PBS: the output

[galaxy-user] Questions about MEME Sequence logo generator

Hi, Has the MEME module been taken out of the main galaxy server? Assuming it'll be back, what's roughly a recommended number of sequences to feed into MEME? It has a limit on the sequences that it can digest but I don't know what it is. Likewise, what's this limit for the Sequence Logo

[galaxy-user] Data sources don't load in Firefox

Hi List, I'm trying to go through Galaxy 101, and the first step is halting me (UCSC Main table browser does nothing on click). I'm giving a presentation on how to use Galaxy, but the data sources do not load when using Firefox. The tool click registers, because the history pane is minimized,

[galaxy-user] error message from Filezilla

Hi, I am getting the following error from the server : Command:USER genebus...@googlemail.com Response:331 Password required for genebus...@googlemail.com Command:PASS *** Response:530 Sorry, the maximum number of clients (3) for this user are already connected. Error: