[galaxy-dev] Problems with Galaxy-Project since 3/14/2013 update

2013-03-18 Thread Zain A Alvi
, Zain Alvi --- PhD Student in Molecular BioSciences Seton Hall University email: zain.a...@student.shu.edu Ph: (973) 710-7149 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions

[galaxy-dev] Same Problems with Galaxy-Project since 3/14/2013 update

2013-03-19 Thread Zain A Alvi
problem of job is waiting to run, but it is not processing. Also, I am having trouble uploading files from NCBI's FTP onto Galaxy-project. I was not experiencing any of these troubles prior to the update to the servers for galaxy-project. Thank you again for looking into this. Sincerely, Zain Alvi

[galaxy-dev] Tophat problem

2013-05-06 Thread Zain A Alvi
Dear Sir or Madam, I hope this reaches you well. Lately, I have been trying to use tophat and then use bowtie on Galaxy project to create an aligned BAM file. The original data came from a SRA file that I have acquired from the Japanese DNA Databank. This SRA was then converted to FASTQ using

Re: [galaxy-dev] Tophat problem

2013-05-20 Thread Zain A Alvi
. The latest GFF is 3.1 on Flybase. I was wondering anyway to convert to a GTF file. Sorry for so many questions. Thank you again for the great help. Sincerely, Zain From: Jennifer Jackson [j...@bx.psu.edu] Sent: Tuesday, May 07, 2013 3:21 PM To: Zain A Alvi Cc