Re: [galaxy-user] GenBank database files

2013-04-29 Thread Peter Cock
On Mon, Apr 29, 2013 at 3:27 AM, Mike Dyall-Smith mike.dyallsm...@gmail.com wrote: Dear Peter Cock, thanks for your advice. Just to be clear, do I leave the files within their decompressed folders or do I put all the individual files into one folder? I assume the former, but want to be sure.

[galaxy-user] List of genomes

2013-04-29 Thread YBao
Hi All, I was trying to map a set of data to a genome, Klebsiella pneumoniae subsp. Pneumoniae MGH 78578(31). While uploading the reads, I was able to find the reference genome as listed above. However, when I tried to map the data using wither bowtie or BWA, the pull down list did not include

Re: [galaxy-user] List of genomes

2013-04-29 Thread Jennifer Jackson
Hello Yongde, The list of genomes is gathered from many sources and is comprehensive to facilitate external display functionality (at UCSC - main and microbial-, Ensembl, Wormbase, etc.). When assigning a dataset in a standard format to one of these sources, those

[galaxy-user] GFF parsing with biopython

2013-04-29 Thread Mic
Hi, I have the following GFF file from a SNAP X1 SNAPEinit 25792712-3.221 + . X1-snap.1 X1 SNAPExon281329454.836 + . X1-snap.1 X1 SNAPEterm 3013303310.467 + . X1-snap.1 X1 SNAPEsngl