[galaxy-user] Screencasts on screencast.g2.bx.psu.edu ?

Hi there I'm trying to download the screencasts referenced in the Galaxy ENCODE paper (Blankenberg et al 2007). They appear to be on screencast.g2.bx.psu.edu, but while that domain resolves, it doesn't respond to HTTP requests. Does anyone know where they are currently available? Thanks, Peter

Re: [galaxy-user] Tophat mapping

I am wondering if these non-coding reads will be included when cufflinks calculates transcript/gene expression. Reads will only be included if they map to assembled/known transcripts. And another question is: how to know the number of reads mapped to a certain exon? This isn't possible

[galaxy-user] Bacterial RNA seq analysis

Dear All I need some (lots) suggestions and help,  first and most important is that i am working on bacterial RNA seq (illumina reads) my analysis steps are as following Step 1.  FASTQ sequence data was groomed Step 2. I did mapping by Bowtie with default parameters. Reference genome

Re: [galaxy-user] Comparing to a single short sequence

Hi Scott, If your Illumina data is DNA, then using either Bowtie (no indels) or BWA (supports indels) with the known sequence as a 'custom reference genome' would be a good choice. If RNA, then doing the same, but using TopHat instead, would be recommended. To use your known sequences as a

Re: [galaxy-user] Tophat mapping

Jeremy, do you have a workflow to estimate what percent of the reads are mapping to unknown expressed regions? Here's a simple approach assuming mapped reads are in BAM format: BAM -- SAM SAM -- Interval Intersect reads as interval with known annotation not allowing for any overlap. Best,

[galaxy-user] Server Erroron Main when viewing or downloading FastQC results

I've run FastQC successfully on several different files, but I can not download them or view them. In either. case I receive the following message in my browser (Firefox): Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here)