galaxy-user July 2013

galaxy-user@lists.galaxyproject.org

37 participants
51 discussions

galaxy online difficulty?
by Elizabeth Clare 15 Jul '13

15 Jul '13

Hi, I've been using galaxy (online) for over a year now without too many issues. Over the last week I can't seem to get anything done. Tasks that normally take seconds are taking overnight and have now stopped entirely. I can't see anything in the twitter feed or news about server maintenance. The types of tools I'm using are simple "reverse compliment" or "barcode splitter" and the data sets are small (some are only a few hundred reads). So these should be very quick tasks. Is there a way I can test whether the problem is at my end? Thanks! fantastic analysis package! Elizabeth -- -------------------------------- Dr. Elizabeth L. Clare School of Biological and Chemical Sciences Queen Mary University of London Mile End Road, London E1 4NS Room 1.02, G. E. Fogg Building e.clare(a)qmul.ac.uk +44 (0)207 882 5687 http://webspace.qmul.ac.uk/eclare/ "If you say yes more often than you say no, you will do interesting things in your life"

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command under the hood
by Kaiyin Zhong (Victor Chung) 14 Jul '13

14 Jul '13

Hi, dear list. We are right now using Galaxy for the pileup of some of our BAM files, but we also would like to be able to use samtools to generating the same results on our own PC. The options we use on the web interface are the simplest, as shown in this screenshot: http://imgur.com/WCwVBvG Can anyone inform us what are the commands and options under the hood? Thanks! Best regards, Kaiyin ZHONG ------------------------------ Forensic Molecular Biology, Erasmus MC k.zhong(a)erasmusmc.nl kindlychung(a)gmail.com

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downloading problems from main Galaxy
by Elwood Linney 11 Jul '13

11 Jul '13

Problem: > when downloading steps in histories back to my computer the files are sometimes incomplete (by incomplete I mean a significantly smaller size that given during the download indicator) Description: >after processing RNAseq files on main Galaxy I have the memory to download steps or complete histories; this past week I have noticed, in a random way that some individual tophat alignments or cuffdiff analyses do not download completely to my computer--sometimes they do, but its random right now Questions: Is there something I can do to eliminate this? Does this have anything to do with how busy Galaxy is? I notice that it sometimes happens even if I try to download one file at a time el linney Duke University Medical Center

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barcode splitter files web based
by Ann Holtz-Morris, M.S. 11 Jul '13

11 Jul '13

HI, I'm trying to use the output files from barcode splitter. I know that the command line as some wrappers made that take the output files and puts them in the history. Is there anything similar for output files but for us biologists who don't do command line? J Thanks, 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.

4 4

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.

2 1

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

2 1

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.

2 1

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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galaxy-user July 2013