Re: [galaxy-user] how to transfer gene id into protein id

2011-10-29 Thread Jennifer Jackson
Hello Victor, RefSeq sequences designated by a transcript identifier formatted as NR_* are non-coding (meaning: transcribed, but not translated), therefore there is no protein product and no linked protein sequence NP_* identifier. This documentation from NCBI covers RefSeq naming

Re: [galaxy-user] how to transfer gene id into protein id

2011-10-29 Thread Hans-Rudolf Hotz
Hi Victor It is not really a Galaxy related answerbut you might wanna study the following webpage explaining the RefSeq Accession Format: http://www.ncbi.nlm.nih.gov/RefSeq/key.html#accession Strictly speaking, there is no such thing as a refseq gene id, since RefSeq entries describe

[galaxy-user] RNA-seq with Staphylococcus aureus strain Newman

2011-10-29 Thread Joe J Harrison
Hello, Would you please add Staphylococcus aureus strain Newman to your database? Workflows to analyze data for genomes available through your database are really simple - but I must admit that I've been struggling with trying to get this to work for a genome (and in particular with the

[galaxy-user] Cufflinks transcript-extract

2011-10-29 Thread dongdong zhaoweiming
Hi,   I use cufflinks to assemble my RNA-Seq reads which produced a GTF file, such as follows:(1)chr1 Cufflinks transcript 6234876 6235400 1000+chr1 Cufflinks exon6234876 6235060 1000+chr1 Cufflinks exon 6235239 6235400 1000+ (2)chr1 Cufflinks