[galaxy-user] fasta-Cuffcompare

2011-09-26 Thread dongdong zhaoweiming
hi, I want to use Cuffcompare to compare my assembled transcripts to a reference annotation. My assembled transcripts is a Fasta format produced by trinity, but Cuffcompare requried GTF file , so what should I do? Thank you! weimin zhao___

[galaxy-user] non-coding RNA

2011-09-29 Thread dongdong zhaoweiming
Hi, I want to evaluate wherther my assembly transcripts produced by trinity is protein-coding or notcoding. I found two methods which are  txCdsPredict program from the UCSC(John R Prensner,2011) and Codon Substitution Frequencies,CSF(Michael F. Lin,2008). I wonder if galaxy can do this? Thanks

[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

[galaxy-user] combine data

2011-11-18 Thread dongdong zhaoweiming
Hi, Can galaxy combine lots of data into a single file using cat? I have a 2GB sam type data, but I can't upload it by URL under my condition, so I want to spilt it into three files and upload it to galaxy and then combine it? Thanks a lot!weimin

[galaxy-user] history was empty

2011-12-05 Thread dongdong zhaoweiming
Hi,   I open my galaxy and found the history was empty, I could not found my previous history, so how can I find it? Thanks a lot!   Reards weimin zhao___ The Galaxy User list should be used for the discussion of Galaxy analysis and other

[galaxy-user] history was empty

2011-12-05 Thread dongdong zhaoweiming
Hi,   I opened  my galaxy and found the history was empty, I could not found my previous history, so how could I find it? Thanks a lot!   Reards weimin zhao___ The Galaxy User list should be used for the discussion of Galaxy analysis and

[galaxy-user] cufflinks-status-FAIL

2011-12-08 Thread dongdong zhaoweiming
Hi,   I used the cufflinks to assemble my SAM file, but the results showed some CUFF's status in not OK,it's FAIL, so that means these CUFF's corresponding sequence  could not used or else mean? Thanks a lot!   Reards weimin zhao___ The

[galaxy-user] find nothing but Workflows

2012-04-12 Thread dongdong zhaoweiming
Hi, I have a problem with galaxy and galaxy test, I find nothing but Workflows All workflows, so what should I do? Thanks a lot! weimin zhao ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features