[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 history: https://main.g2.bx.psu.edu/u/sheenams/h/clone-of-s1jaf13mir-active-items-only Thanks Sheena___ 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 replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[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 that only 1/5 reads were left. Can anybody tell me if this operation is proper?? How do you normally optimize the mapping rerults from Tophat? Which considerations should I take into account? Looking forward to your reply. Jiwen ___ 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 replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[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 or span exons (splice junction). These reads seem to fit very well. However, I can also see a lot reads mapped to non-coding region. Are these reads from pre-mRNA? or my mapping was wrong? Did anybody have similar experience?? Furthermore, I can see huge enrichment of reads in 3' UTR (much much more than the coding region). Is this normal? Is this caused by the rRNA depletion method ? Looking forward to your reply Jiwen ___ 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 replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[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___ 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 replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[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 300bp, where each end is 50bp, you should set -r to be 200. There is no default, and this parameter is required for paired end runs. I think the size of fragment (here 300bp) includes not only the length of pair end reads, but also the length of adaptors. so, maybe the Mean Inner Distance between Mate Pairs should be : fragment length - pair end read length - adaptor length. Am I right? or did I miss something? Is it a must to type in the accurate value? Looking forward to your reply JIwen ___ 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 replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[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 ID and transcript ID. What I did is: I run cufflinks using reference gene sets (GTF file) from Ensembl (see picture human Chr19 refgene). I modified the ensembl GTF file according to http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq#faq4 so that cufflinks can recognize the column for chromosomes. I got cufflinks assembled transcript which shows nicely the gene ID, transcript ID (see picture Cufflinks assembled transcript), but the gene name was lost in this file. Then I run cuffcompare using the same reference gene sets (GTF file) from Ensembl. In the output file (picture cuffcompare combined transcript) you can see that gene name appeared, but galaxy assigned new ID to gene and transcript. Then I run cuffdiff . Output file (see picture Cuffdiff transcript differential expression) only contains gene name. My question is: how can I keep the information from the reference gene sets during the whole analysis process so that I get meaningful information. Or it is that possible that I retrieve gene ID, transcripte ID by using the output file Cuffdiff transcript differential expression from cuffdiff? I hope you can help me. Many thanks in advance. JIwen___ 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 replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[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 calculated from the mapped reads. However, I think cufflinks only uses accepted hits as input, maybe it is not a big problem that splice junction' is not accurate. Am I right? Was there something wrong when I mapped my reads with tophat? Hope you can help me figure it out. Looking forward to hearing from you. Jiwen ___ 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 replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[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 decrease after I delete files permanently. DId I miss something? How to let the record show the real size of the histories? Thanks in advance. Greetings, Jiwen___ 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 replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
