[galaxy-user] Reference genome , fasta with or without gene feature

Dear All I am analysing bacterial RNA seq (illumina). as my reference genome is not in galaxy. so i need to downlaoded the reference genome from  NCBI and upload to my history Should i use reference genome with  gene features or  single  fasta file with out any annotation information. even

[galaxy-user] Bacterial RNA seq analysis

Dear All I need some (lots) suggestions and help,  first and most important is that i am working on bacterial RNA seq (illumina reads) my analysis steps are as following Step 1.  FASTQ sequence data was groomed Step 2. I did mapping by Bowtie with default parameters. Reference genome

[galaxy-user] Cuffdiff

using sample 1 as transcripts are not the same when i am suing sample 2 as transcript i am bit confused what should be the correct way any help is very much welcomed Best ateeq   Ateequr Rehman House No. 2 ground floor Blauenstr. 10 79115 Freiburg im

[galaxy-user] Disk space quota Issue

Dear Administartor My disk space quote is full, is their any way to increase it,or only way is delete some files... Best Ateeq   Ateequr Rehman House No. 2 ground floor Blauenstr. 10 79115 Freiburg im Breisgau

[galaxy-user] Cuffdiff result P and q values

no   Ateequr Rehman House No. 2 ground floor Blauenstr. 10 79115 Freiburg im Breisgau___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all

[galaxy-user] ILLumina 1.9 Hiseq

Dear Glaxy users and admin I ran my sequence data on FASTQC tool, output says it is EncodingSanger / Illumina 1.9 now i want to groom my file, but groomer does not have option for 1.9 in Input FASTQ quality scores type any idea which option i should select to grroom my file, later i

Re: [galaxy-user] Cufflinks related problem

Dear Bomba I am bit confused , Are you running bowtie --- tophat Cufflink For bowtie run you are using reference genome annotation  in gff3 format  I am curremntly totally unable to figure it out correctly, how i should analyse my RNA seq data Best Ateeq  

Re: [galaxy-user] Using galaxy for Bacterial RNA-seq

Dear Noa and Bomba i am also in situation like you, hardly any programming experiance but want to analyse, bacterial tranmscriptome before and after an stress. I am very new to galaxy, would be obliged if any one can give me more hints, i have few queries In Brief;  we did our sequnecing by

[galaxy-user] genome for Stenotrophomans

Dear Galaxy AdministratorI am analysing transcriptome and genome of clinical isolatesStenotrophomonasmaltophilia, would be highly obliged if you could please upload Stenotrophomonas maltophilia K279 and Stenotrophomonas maltophilia R551-3 genome acccesion numbers at NCBI are as following

[galaxy-user] data upload

Dear galaxy UsersI am very very new to galaxy, will be highly obliged if some one could help me to find the way to analyse bacterial tramnscriptome. in the first step itself , i am having trouble to upload files...Does any one knows how to generate URL to upload data, my fastq files are about 3 gb