[galaxy-user] Help!! Tophat paired end reads

Hi, I am very confused by my mapping. Please help me figure out what's wrong with my operation. I got Illumina Hiseq 2000 paired end reads (mouse), and I used Tophat to map these reads. After mapping, I used IGV to have a look at the mapping. I can see that some of the reads fall into exons o

Re: [galaxy-user] Editing workflows : Server error ?

Hi Sandrine, Thanks for sending the workflow link. A correction to this specific problem has been made (changeset 7038:1fdcce63a06f at https://bitbucket.org/galaxy/galaxy-central). This will reach the public main instance at the next update (likely within a week or so). The version of Galaxy

Re: [galaxy-user] Help!! Tophat paired end reads

Hi Jiwen, The bioinformatics part of your analysis sounds as if it went fine, so that is good news. This list may not be the best place to get feedback about library construction methods, but we can see who has help to offer. I did a quick search myself and found this recent publication that

[galaxy-user] Tophat mapping

Hi, After mapping RNA-Seq paired end reads with Tophat, I can see that most of reads fall into the right regions. However, I still can see lots of reads mapped to non-coding region (the locations where the reads are mapped to don't contain exons). I am wondering if these "non-coding reads"