- galaxy-user - lists.galaxyproject.org

Get Gene name from Cuffdiff's output?
by Hoang, Thanh 17 Jun '13

17 Jun '13

Hi guys, I am trying to examine gene differential expression in my mouse samples using : Cufflink >> Cuffmerge>>Cuffdiff The output from Cuffdiff shows only gene id, but not gene name: test_id gene_id genelocus sample_1 sample_2 XLOC_000001XLOC_000001- 1:3200263-3200566EpitheliumFiber Could anyone tell me how to make the gene name show up? I used Mus_musculus.GRCm38.71.dna.toplevel.fa as the reference sequence (not GRCm38/mm10 from UCSC table broswer because i think this may be old version). I have been trying to find a solution online but still very confused Thanks so much Thanh

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chimeric reads detection
by Delattre Hadrien 17 Jun '13

17 Jun '13

hello, I am a beginner Galaxy user and I need to perform chimeric sequences detection on single end reads (from metatranscriptomic samples). Do someone know a tool for that? thanks hadrien

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BWA failing to index?
by Joshua Orvis 17 Jun '13

17 Jun '13

I just installed a new instance of Galaxy and bwa_wrappers from the main toolshed. I then uploaded a reference genome along with two FASTQ files in order to run "Map with BWA for Illumina". When I run it, I get this error: The alignment failed. Error aligning sequence. [bwa_aln] 17bp reads: max_diff = 2 [bwa_aln] 38bp reads: max_diff = 3 [bwa_aln] 64bp reads: max_diff = 4 [bwa_aln] 93bp reads: max_diff = 5 [bwa_aln] 124bp reads: max_diff = 6 [bwa_aln] 157bp reads: max_diff = 7 [bwa_aln] 190bp reads: max_diff = 8 [bwa_aln] 225bp reads: max_diff = 9 [bwt_restore_bwt] fail to open file '/export/galaxy-dist/database/files/000/dataset_1.dat.bwt'. Abort! Aborted I've used the same tool on other Galaxy instances and it always auto-indexes the reference genome here before continuing. What's going wrong? (I made sure bwa was in the user's PATH that is running run.sh)

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fastq-dump on sra files from NCBI
by Murphy, Theresa 17 Jun '13

17 Jun '13

Is it possible to upload files from the NCBI sra data base, then use fastq-dump from the sra toolit within galaxy? If not, could these tools be added? 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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(no subject)
by Loubna Youssar 17 Jun '13

17 Jun '13

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can galaxy analyze SOLiD XSQ dataset except csfasta/qual data?
by Wang, Daqing 15 Jun '13

15 Jun '13

Hello, I wonder if Galaxy take SOLiD XSQ format data as input for mapping. I know it takes csfasta/qual data. Does anyone try this kind of analysis with SOLiD XSQ format? Any feedback and advice is appreciate it. Thank you! Daqing Wang

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genomic coordinates to Enterz gene ids
by shamsher jagat 15 Jun '13

15 Jun '13

I have a list of around 3000 genomic coordinates of mouse genome and I would iike to extract gene name Enetrz gene ids Is it possible to extract this information in galaxy. Thanks Kanwar

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visualization problems
by Ann Holtz-Morris, M.S. 13 Jun '13

13 Jun '13

Hi, Earlier today I couldn't add a new visualization. I just was working again and now I cannot load the viualizations that I'd previously set to load (BAM from SAV). I get the message Internal Server Error Galaxy was unable to sucessfully complete your request.... GURU MEDITATION: #ff39a25b2b684850ba01c9bdc9eb8942 Thanks for your help! Ann Ann Holtz-Morris SRA III de Jong Laboratory CHORI Oakland Oakland, CA

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another newbie question
by Boaz Shaanan 13 Jun '13

13 Jun '13

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Isochore as Genome coordinates ?
by Abdullah Al Mahmud 13 Jun '13

13 Jun '13

Hi, In my account I have uploaded a file name iso_mm10.bed. The bed files contains coordinates of 6018 isochores of mouse genome mm10. I want to extract GC% of each scores with the list of genes present in each isochores. I tried using extract features, geecee, and many other tools from galaxy. But every time either it said error or no peak. I will be grateful to you if you kindly give me an idea about how to solve this problem. Abdullah -- Abdullah Al Mahmud, PhD Postdoctoral fellow, University of Montreal, Lab. of Dr. Jacques Michaud CHU Sainte-Justine Research Center, Montreal, Quebec, Canada. abdullah.al.mahmud(a)umontreal.ca

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