Re: [galaxy-user] Getting the installed data to show up in the sample files at run time

On Fri, Jul 6, 2012 at 3:07 AM, Aarti Desai wrote: > These show up in the history with the appropriate size. But when I choose > the “Map with BWA for Illumina” option, the two fastq files do not show up > in the FASTQ file drop down. Hi Aarti, Most tools in galaxy that work with fastq file need

[galaxy-user] Tophat

Hello, Using the defaults and then testing the resulting SAM output seems to be what most folks are doing if they do not have access to the original library construction methods (e.g. size selection). Both SAM Tools and Picard are in Galaxy. This is a useful post where the options are discuss

[galaxy-user] fetch codons and amino acid

Hi all, I am a new Galaxy user and I have searched the mail list, looking for the answers to my questions, but failed. I am trying to fetch the corresponding codon or amino acid alignments among 46 species using genomic intervals in human. I know if I have a list of human genomic intervals, I

[galaxy-user] Question about SICER out put

I used SICR to call peaks and have following out put files: 1. test.1removed bed 2. control1 removed .bed 3. test w 200 graph 4. test w200 normalized graph 5. test w200-G600 FDR.05 island.bed 6. test w200-G600 FDR .05 island filtered.bed 7. test w200-G600 FDR .05 island filtered normalized.wig 8

Re: [galaxy-user] fetch codons and amino acid

Hi Patricia, If your data is still in MAF format, first convert it to FASTA using the tool "Convert Formats -> MAF to FASTA". Next, translate the regions using the tool "EMBOSS -> transeq". Depending on where your intervals are located, the data may get confusing at the translation step if y