[galaxy-user] fasta-Cuffcompare

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___ T

[galaxy-user] non-coding RNA

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? Thank

[galaxy-user] version tophat and cufflinks

Hi,   May I ask what is the version of TopHat and cufflinks in the galaxy? Thanks a lot! weimin zhao___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please

[galaxy-user] select tophat and cufflinks

Hi,   I'm a user of galaxy.As I know, when TopHat and Cufflinks are supported through Galaxy, its version is 1.1.1 and 0.9.3,respectively. But now, the present version of TopHat and cufflinks is 1.3.2 and 1.1.0, which have some  improvement over the previous version. I have a RNA-Seq reads about

[galaxy-user] cufflinks set parameters

Hi,   It's the first time for me to use cufflinks in galaxy, two choices confused me as follows: Perform Bias Correction: No Yes Bias detection and correction can significantly improve accuracy of transcript abundance estimates. Set Parameters for Paired-end Reads? (not recommended): No Yes

[galaxy-user] Cufflinks transcript-extract

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

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 zhao

[galaxy-user] history was empty

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 fea

[galaxy-user] history was empty

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 othe

[galaxy-user] cufflinks-status-FAIL

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 Ga

[galaxy-user] find nothing but Workflows

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