[galaxy-dev] Mutation/SNP detection RNA-Seq

Hi, I am trying to look mutations/SNPs in RNA-Seq data. Can anyone suggest me a workflow in Galaxy on how to detect SNPs and mutations Thanks in advance Suz ___ Please keep all replies on the list by using reply all in your mail client.

[galaxy-dev] cuffdiff output

Hello, I am new to using Galaxy tools. I am running paired end RNA-Seq data on Galaxy and I want to differential gene expression between control and treated samples I was fine until running TopHat output, I am having problems with cufflinks and cuffdiff output. I ran the cufflinks and cuffdiff

[galaxy-dev] File upload via ftp: FileZilla

Hello everyone, I am trying to upload files (size:6GB) via ftp and i am using FileZilla for ftp upload of files. Host/usernames and password details as follows: Host: main.g2.bx.psu.edu Username: My galaxy Username Password: Galaxy password I found this tutorial for FTP upload.

[galaxy-dev] TopHat paired end

Hello, I am trying to do RNAseq analysis on Paired end data Illumina. I have about 4 files for each sample (2 forward and 2 reverse). I want to analyze the data in Galaxy. Do I have to groom and run the QC for each file? Should I join the paired files and run both tools on each pair, or should

[galaxy-dev] TopHat for paired end

Hello, I am trying to run TopHat for paired end and this is my first time using Galaxy and TopHat and I have a doubt regarding what to mention in Mean Inner Distance between Mate Pairs:The default value is 20. Should I leave the value or should I be changing the value. What is Mean Inner

[galaxy-dev] TopHat fusion

Hello, Is there any plan of installing TopHat fusion in Galaxy in near future. Thanks Katie ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists,