[galaxy-dev] RNA-seq
Hi, My name is Karla Fernández a student of a University in Nuevo Leon in Monterrey, Mexico (UANL). The reason for this mail is because i'm going to work with differential gene expression of the yeast Pichia pastoris and i'd seen that the complete genome and annotations of this yeast are absent in programs like bowtie, tophat and cufflinks, I wondered if it might be possible to upload the genome and annotations of these yeast for my DGE. Thank you so much QBP. Karla Fernández Cano ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] RNA-seq wig file from UCSC conversion to gene expression values, using Galaxy
Hello Galaxy list, I'm helping a student with a human bioinformatics project. We would like to generate a single relative gene expression value for each gene in the human genome (for different cell lines of interest) using the RNA-seq data from the UCSC archive. We can see raw signal values by displaying the following file as a track in the Genome Browser: Track name: BJ cell pA+ + 1 Table name: wgEncodeCshlLongRnaSeqBjCellPapMinusRawSigRep1 File name: /gbdb/hg19/bbi/wgEncodeCshlLongRnaSeqBjCellPapPlusRawSigRep1.bigWig But where we get stuck is trying to import the wig into Galaxy to generate expression values for each gene. Cufflinks seems like the right tool for the output we want, but we're not sure what the inputs are supposed to be. We'd appreciate any help you can provide. Best regards, ---Karmella ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
