October 2011 - galaxy-user - lists.galaxyproject.org

Get only repeatmasked exons
by Managadze, David (NIH/NLM/NCBI) [F] 20 Oct '11

20 Oct '11

Dear Galaxy expert(s), I have .BED file of regions from mouse. I guess many of them can span whole genes i.e. many exons; might even span over the gene flanks. I need to get the REPEATMASKED sequences of only the annotated exons of these regions. I see that If I use the tool "Fetch Sequences->Extract Genomic DNA" on these regions, it returns sequences with mixed small and capital letters. Question I: what are the small letters and what are the capitals here? Are these already masked, exons/introns or what? (I downloaded some of these sequences and repeatmasked myself. My pasked sequences overlap with some of "yours" written in small letters.) Question II: Is the strand "honored" by these tool? I guess I remember from my old experience that there was an issue although I can not recall what exactly. Thank you in advance, David

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save/export image from workflow editor?
by Casey Bergman 20 Oct '11

20 Oct '11

Dear Galaxy Team - [Apologies if this has been answered before on this list before...I couldn't find anything related via google] Is there a way to save/export an image of the workflow shown in the workflow editor? Best regards, Casey

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Issue about uploading data
by Nandan Deshpande 20 Oct '11

20 Oct '11

Hi, My user id is "deshpandenandan1975(a)gmail.com". I have been trying to upload 2 files each around 650 MB in size but the upload is in process for last 15 hrs .. I had a similar problem in uploading data to Galaxy few months back and had to give up using the tool. Can u suggest me a way out? cheers, Nandan

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Zoom function on workflow editor?
by Arthur Goldberg 20 Oct '11

20 Oct '11

Hi Galaxy's cool! Is there a zoom function on the workflow editor? (I know about hiding nodes from the tutorial <http://main.g2.bx.psu.edu/galaxy101>.) Thanks Arthur -- Senior Research Scientist Computational Biology Memorial Sloan-Kettering Cancer Center cBio Cancer Genomics Portal <http://www.cbioportal.org/>

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bed12 format for stitching blocks given a set of coding exon intervals
by Amit Indap 20 Oct '11

20 Oct '11

Hi Galaxy, I am trying to stitch together MAF alignments for the coding sequence for a few genes of interest in Drosophila. I used UCSC to send the bed intervals of the coding exons of my gene and sent the output to Galaxy. But when I try and use the tool "Stitch Gene blocks" it complains that my bed is a bed3 and not a bed12. I'm a bit rusty with my browser skills, but how can I send my output to Galaxy as a bed12 format so I can stitch my MAF blocks together? Thanks for your help! Amit -- Amit Indap

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Query regarding RNA-Seq data analysis
by santhi ramachandran 19 Oct '11

19 Oct '11

Hi, I am having a fastq file for my RNA data analysis in my computer. How to make it available for RNA seq data analysis using tophat. Sandy

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Posting in the List
by santhi ramachandran 19 Oct '11

19 Oct '11

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How to combine two Reference Genome (Files) In Galaxy?
by Binbin You 18 Oct '11

18 Oct '11

Hi all, I have two reference (genome) files. Let's say EAB_FB_MG.fa(total37972 sequences/contigs) and EAB_FB.fa(21272 sequences/contigs). I know there are some common contigs between them. How could I combine/merge them to get a new reference file with all unique contigs (without duplicates)? Many thanks for any idea!!

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Regarding perl script
by Shambhavi Srivastava 18 Oct '11

18 Oct '11

Hello all, I am a new to GALAXY and am trying to create my own workflow with my own scripts written in PERL and integrating it with few already available in GALAXY. I tried the basic example given in GALAXYwiki..the program about counting GC content. I followed all the steps mentioned but when I start my galaxy server I dont see myTools option and even the pre installed options like GetData and all dont appear on screen. What should I do...can anyone send me another or a step by step procedure of how can I run my programs. Thankss..

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Memory issues while using Galaxy
by prashant singh 18 Oct '11

18 Oct '11

Hi We have installed Galaxy on a local machine (Mac pro 2 x 2.4 gHz quad core Intel Xeon with 32 GB RAM). We wish to use dynamic trimmer in order to trim the data and while downloading a groomed file from galaxy, it runs out of memory. Please advise. Sent from my iPhone

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