[galaxy-user] Tophat mapping error

Hi all, I got the following error infomation during Tophat mapping An error occurred running this job: Job output not returned by PBS: the output datasets were deleted while the job was running, the job was manually dequeued or there was a cluster error. Please let me know what's wrong. Help

[galaxy-user] Jobs in queue

I have similar problems. My tophat job was sent 6 hours ago. Now the job is still waiting to be run. Jiwen Hi, My cufflinks jobs sat in the queued state for 12+ hours so I restarted them this morning. They've been in the queued state now for about 2-3 hours. Any idea why? Here's a link to my

[galaxy-user] Help!!! cuffdiff log2 value

Hi, I am analyzing my RNA-Seq data. After running cuffdiff, I got a list of differentially expressed transcrpts or genes. As far as I know, log2 value = fold change. However, there are minus values. Is this possible?? log2 value can not be minus. Did I miss something?? Looking forward to you

[galaxy-user] cuffcompare or cuffmerge

Hi all, I read one paper "Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks". They say the procedure for RNA-Seq analysis is Tophat-->cufflinks-->cuffmerge-->cuffdiff But what I normally do in Galaxy is Tophat-->cufflinks-->cuffcompare-->cuff

[galaxy-user] Mapping paired end reads with Tophat

Hi all, After mapping, I used IGV to have a look at the mapping. There are a lot of mapped reads without pair reads. Should I keep these reads? or Is this a problem for cufflinks analysis? What I tried is: 1. BAM to SAM 2. Filter SAM: set Read mapped in a proper pair to Yes. The result is tha

[galaxy-user] Tophat mapping

Hi, After mapping RNA-Seq paired end reads with Tophat, I can see that most of reads fall into the right regions. However, I still can see lots of reads mapped to non-coding region (the locations where the reads are mapped to don't contain exons). I am wondering if these "non-coding reads"

[galaxy-user] Help!! Tophat paired end reads

Hi, I am very confused by my mapping. Please help me figure out what's wrong with my operation. I got Illumina Hiseq 2000 paired end reads (mouse), and I used Tophat to map these reads. After mapping, I used IGV to have a look at the mapping. I can see that some of the reads fall into exons o

[galaxy-user] Help!! Uploading with FTP

Hi, I am uploading files to Galaxy via FTP. The speed is only 30kb/sec. Is there something wrong with my operation? or is this just normal due to Galaxy's work load? Looking forward to your answers. Thanks Jiwen ___ The Galaxy User list sh

[galaxy-user] Tophat paired end read

Hi all, I have paired end RNA-Seq reads ( Illumina Hiseq 2000) in seperate files. Before mapping, I need to trim the reads. My questions is : Do I have to join pair end reads before timming, and then split again for Tophat??? Lookiong forward to your answers. Thanks Jiwen ___

[galaxy-user] Job running speed is really slow

Dear Galaxy team, I found glalaxy (website) is running really slow today. I just did some text manipulations over a very small file. It takes a long time till the gray colour (waiting) turns into yellow (running). Now the jobs are still waiting to be processed (gray colour). I have to analyz

[galaxy-user] Tophat

Dear all, This might be a silly question, but I couldn't figure it out by myself :-((. Could you please tell me how I can find out how many reads have been mapped to the genome after running Tophat for pair end RNA seq data? Thanks in advance. JIwen_

[galaxy-user] Tophat "Mean Inner Distance between Mate Pairs"

Hi all, When mapping pair end RNA-seq reads using tophat, we need to type in "Mean Inner Distance between Mate Pairs". In galaxy, we can read the following information: This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments selected at

[galaxy-user] RNA-Seq analysis

Since the pictures are too big for the mailling list. I will upload it in seperate emails. Dear all, I am using Galaxy for RNA-Seq analysis. I expect two lists: differentially expressed transcripts and differentially expressed genes. In these two lists, I would like to see the gene name, gene

[galaxy-user] Tophat

Dear all, Today I used Tophat to map the reads from RNA-Seq, and had a look at the results using "visaulization" function. In some regions I can see splice junctions calculated by Tophat, but I don't see any reads mapping to this region. Is this a bit strange? I thought "splice junction" is calc

[galaxy-user] The size of the history

Hi all, First I would like to thank you for your fast replies to my questions. As you know, at top right corner of Galaxy window, there are records of the history size and how many percentage of memory space has been used. I found that the number in the records only increases, but doesn't decreas

[galaxy-user] A simple operation didn't work out

Hi All, I got a bit disappointed when I failed in the following operation which seems to be simple. I uploaded mouse annotation/reference gene sets (GTF format) to Galaxy. The file is located at ftp://ftp.ensembl.org/pub/release-65/gtf/mus_musculus/. As far as I know, GTF file is t

[galaxy-user] FTP and Biomart

Hi All, Today I have problem to use FTP to upload data to Galaxy. I used Filezilla software and the server name "main.g2.bx.psu.edu", but I can not connect to the server. Something wrong with my operation? Also, when I tried to get data from Biomart to Galaxy, I got the error warning "the up

[galaxy-user] Gene and transcript names from Cuffdiff

Hi all, I am learning how to use Galaxy to analyze my RNA-Seq data. After running cuffdiff, one of the files I got is "transcript differential expression testing". In this file, I can see " gene_id" is something like "XLOC_01". I am wondering how I can find the name of differentially expre