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Cuffmerge error: duplicate GFF ID encountered
by Delong, Zhou 09 Jul '13

09 Jul '13

Hello, I was doing a RNA analyse and I wished to compare the transcription and expression of two samples using a reference annotation, however this is the error message I got: =====Quote===== Error running cuffmerge. [Thu Jul 4 07:32:59 2013] Beginning transcriptome assembly merge ------------------------------------------- [Thu Jul 4 07:32:59 2013] Preparing output location cm_output/ [Thu Jul 4 07:34:07 2013] Converting GTF files to SAM [07:34:07] Loading reference annotation. [07:34:07] Loading reference annotation. [Thu Jul 4 07:34:08 2013] Quantitating transcripts You are using Cufflinks v2.1.1, which is the most recent release. Command line: cufflinks -o cm_output/ -F 0.05 -g /galaxy/main_pool/pool7/files/006/446/dataset_6446730.dat -q --overhang-tolerance 200 --library-type=transfrags -A 0.0 --min-frags-per-transfrag 0 --no-5-extend -p 4 cm_output/tmp/mergeSam_fileIO17rb [bam_header_read] EOF marker is absent. [bam_header_read] invalid BAM binary header (this is not a BAM file). File cm_output/tmp/mergeSam_fileIO17rb doesn't appear to be a valid BAM file, trying SAM... [07:34:08] Loading reference annotation. [07:35:53] Inspecting reads and determining fragment length distribution. Processed 33854 loci. > Map Properties: > Normalized Map Mass: 8719.00 > Raw Map Mass: 8719.00 > Fragment Length Distribution: Truncated Gaussian (default) > Default Mean: 200 > Default Std Dev: 80 [07:35:53] Assembling transcripts and estimating abundances. Processed 33854 loci. [Thu Jul 4 07:39:29 2013] Comparing against reference file /galaxy/main_pool/pool7/files/006/446/dataset_6446730.dat You are using Cufflinks v2.1.1, which is the most recent release. Error: duplicate GFF ID 'ENST00000361547.2' encountered! [FAILED] Error: could not execute cuffcompare ======End quote====== The job goes well without the annotation reference. The annotation file I used can be downloaded here: ftp://ftp.sanger.ac.uk/pub/gencode/release_17/gencode.v17.annotation.gtf.gz Can anyone help me please? Thanks, Delong

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problem uploading bam and bai files
by Ann Holtz-Morris, M.S. 09 Jul '13

09 Jul '13

Hi, I've searched the archives and cannot find my situation. I have an Illumina MiSeq dataset with ~8 million reads that was aligned to the reference genome on the MiSeq machine. (The machine uses BWA to allow overlapping reads, unlike Casava.) The alignment generated dataset.bam and dataset.bam.bai files in the same directlry. I used Get Data to upload both files. The problems, possibly related, are that Galaxy 1) would not recognize the .bam file as a bam file and 2) would not recognize the dataset.bam.bai file as the bam file metadata. After uploading the bam file, originally identified as a text file, I manually used the pen option to tell Galaxy that the data was a .bam file. I then uploaded the .bam.bai file. The data would not display the data at UCSC genome browser nor in Trackster, even though those options were displayed for the .bam file. After uploading, I also used the pen editor to change from dataset.bam.bai to dataset.bai. None of these options worked for Trackster, UCSC genome brower, nor IGV nor IGB. Interestingly, IGV would display it if the data was used directly form my hard drive but not through Galaxy. Any advice would be greatly appreciated. Ann CONFIDENTIALITY NOTICE: This electronic message is intended to be for the use only of the named recipient, and may contain information that is confidential or privileged. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is strictly prohibited. If you have received this message in error or are not the named recipient, please notify us immediately by contacting the sender at the electronic mail address noted above, and delete and destroy all copies of this message. Thank you.

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hg19 with rCRS
by rabab khairat 09 Jul '13

09 Jul '13

Dear Galaxy,Before the new modifications, i was using hg19 human genome with the rCRS mitochondrial genome for mapping. but now i can't recognize it from the hg19 genomes in the genomes drop-down list.could you please help me, which one is with rCRS.my kind regards Rabab Khairat

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elandmulti format
by Murphy, Theresa 09 Jul '13

09 Jul '13

Using the Galaxy public server, Is it possible to do peak calling using MACS on Bowtie mapped paired end reads if I do not have access to ELAND to generate ELANDMULTI format. The illumina reads were originally downloaded from the SRA database rather than being generated in house. Is it possible to convert the Bowtie output to ELANDMULTI format? Thanks, Theresa Murphy The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.

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Regarding galaxy wrappers: "lumi", "DESeq" "edgeR"
by Sachit Adhikari 08 Jul '13

08 Jul '13

Hi, These are the R libraries. Have anyone written a wrapper for these libraries "lumi", "DESeq" "edgeR"? Thanks, Sachit

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How to define the cutoff value of RPKM for expressed genes?
by Hoang, Thanh 04 Jul '13

04 Jul '13

Hi all, I have been working on RNA-seq data analysis using TopHat and Cuffdiff. One of the problem I have is to define the cutoff RPKM value to tell whether a gene is expressed from the background noise?. Could anybody give me a suggestion? Thank you Thanh

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Problem with ftp server?
by Katrien M. Devos 01 Jul '13

01 Jul '13

I successfully uploaded files to the main Galaxy server this morning using ftp. However, any attempts to upload files since around noon have failed. I get a 'Could not connect to server' error when trying to connect to main.g2.bx.psu.edu uisng FileZilla. Any suggestions? Thank you. Katrien -- Katrien M. Devos Dept. of Crop and Soil Sciences & Dept. of Plant Biology University of Georgia Athens, GA 30602 USA Tel: (706) 542-0925 Fax: (706) 542-0914 E-mail: kdevos(a)uga.edu

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(no subject)
by Dave Clements 30 Jun '13

30 Jun '13

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Re: [galaxy-user] galaxy-user Digest, Vol 84, Issue 27
by Batool Akhtar-Zaidi 28 Jun '13

28 Jun '13

Please unsubscribe Sent from my iPhone On Jun 28, 2013, at 12:01 PM, "galaxy-user-request(a)lists.bx.psu.edu" <galaxy-user-request(a)lists.bx.psu.edu> wrote: > Send galaxy-user mailing list submissions to > galaxy-user(a)lists.bx.psu.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.bx.psu.edu/listinfo/galaxy-user > or, via email, send a message with subject or body 'help' to > galaxy-user-request(a)lists.bx.psu.edu > > You can reach the person managing the list at > galaxy-user-owner(a)lists.bx.psu.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of galaxy-user digest..." > > > HEY! This is important! If you reply to a thread in a digest, please > 1. Change the subject of your response from "Galaxy-user Digest Vol ..." to the original subject for the thread. > 2. Strip out everything else in the digest that is not part of the thread you are responding to. > > Why? > 1. This will keep the subject meaningful. People will have some idea from the subject line if they should read it or not. > 2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative. > > Today's Topics: > > 1. Re: gft annotation files (Jennifer Jackson) > 2. Re: Pause function please (Jennifer Jackson) > 3. Problem with ftp server? (Katrien M. Devos) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 27 Jun 2013 11:12:38 -0700 > From: Jennifer Jackson <jen(a)bx.psu.edu> > To: Vijay Kumar <nayaganviji(a)gmail.com> > Cc: galaxy-user(a)bx.psu.edu > Subject: Re: [galaxy-user] gft annotation files > Message-ID: <51CC8096.2030802(a)bx.psu.edu> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" > > Hello, > > The UCSC Table browser can be used to extract a GTF file formatted > dataset. See the tool "Get Data -> UCSC Main". The output format is one > of the choices at the bottom of the tool UCSC form and there is a user > guide below that at the UCSC web site that details how-to for queries. > > Best, > > Jen > Galaxy team > > > On 6/27/13 4:35 AM, Vijay Kumar wrote: >> Dear sir, >> any one suggest me where i download reference annotation gft files for >> zebra finch . i tried ucsc site, but i donot know exact place to get >> gft files. thank u sir.......... >> >> >> ___________________________________________________________ >> 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/ >> >> To search Galaxy mailing lists use the unified search at: >> >> http://galaxyproject.org/search/mailinglists/ > > -- > Jennifer Hillman-Jackson > Galaxy Support and Training > http://galaxyproject.org > >

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Pause function please
by Ann Holtz-Morris, M.S. 27 Jun '13

27 Jun '13

Hi, I read https://www.google.com/url?q=http://dev.list.galaxyproject.org/Can-t-find-n… <https://www.google.com/url?q=http://dev.list.galaxyproject.org/Can-t-find-n…> &sa=U&ei=KFzLUaHFCaGcjALSq4GQCw&ved=0CAcQFjAA&client=internal-uds-cse&usg=AFQjCNHSziHrbCCmumvDDUtmAeW9RvLRdg with interest. I would also like a Pause function as a toggle on/off so I can stop look at the data being generated. I'm running a BWA alignment that's been working now for almost 48 hours. It's a decent sized data set but it had a very low quality second sequencing read. I've quality trimmed and length filtered. It ended up being only ~50% of the # of reads in Read1. I'd love to be able to pause it and see if the data set is behaving as expected. Thanks, Ann Ann Holtz-Morris SRA III de Jong Laboratory 510-428-3885 x 5715 aholtzmorris(a)chori.org Shipping and Mailing Address Attention: Ann Holtz-Morris CHORI-BACPAC Resources BLMR Bldg. 747 52nd St. Oakland, CA 94609-1809 CONFIDENTIALITY NOTICE: This electronic message is intended to be for the use only of the named recipient, and may contain information that is confidential or privileged. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is strictly prohibited. If you have received this message in error or are not the named recipient, please notify us immediately by contacting the sender at the electronic mail address noted above, and delete and destroy all copies of this message. Thank you.

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