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

Calling SNP's
by sukeerthi teja Rallapalli 17 May '11

17 May '11

Hi, Is it possible to convert a fasta file to sam/bam format using galaxy. ? OR Is is possible to call SNP's using Blast 2.2.25 (Stand Alone Blast) Thank you Teja

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Reload ".loc" files without restarting the Galaxy server?
by Luobin Yang 17 May '11

17 May '11

Hi all, I am wondering if it's possible to to reload a ".loc" file without restarting the Galaxy server? Thanks, Luobin

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problem with filter RNA-seq
by shamsher jagat 17 May '11

17 May '11

I have tried to follow the steps: File 33 in my history is generated by using filter GTF data by attributes. Two files used were file 29 which is a splicing diff file filtered for yes and file 2 is combined GTF. I used TSS-id for filtering. the out put file file 32 is empty. Any suggestion? Jagat, It depends what filter tool you're using and what dataset you're filtering. There is a generic filter tool that can be used to filter Cuffdiff tabular files for either FPKM values and differential expression tests. There is also a tool for filtering GTF files based on a Cuffdiff expr dataset. It sounds like you may be confusing either the tools or the inputs. If after double-checking you're still having problems with filtering, please put together a short list of your analysis steps and share your history with me, and I can take a look. Thanks, J. Further to my question, It appear that there is some problem with the filter option: When I use the isoform/gene exp file as such it work fine but when I filter these files with either parameter such as status if test was successful or on p value it return me empty file. The way am saving the file is - expr file filter save as txt file and upload back in Galaxy. Any suggestion? Jagat

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Re: [galaxy-user] Calling SNP's
by Jennifer Jackson 16 May '11

16 May '11

Hello Teja, Exploring the "Pages" tutorials is recommended as many have SNP-specific analysis examples. I am not sure if your data is RNA or DNA or if you have quality scores available, but there are tutorials that cover most common-use cases. http://main.g2.bx.psu.edu/page/list_published It is recommended to start with these: http://main.g2.bx.psu.edu/u/aun1/p/screencasts http://main.g2.bx.psu.edu/u/james/p/exercises http://main.g2.bx.psu.edu/u/aun1/p/galaxy101 Good luck with your research! Best, Jen Galaxy team ps: For next time, please keep the galaxy-user cc so that our entire team can contribute to replies. This would be especially helpful when you have a new question. On 5/16/11 11:53 AM, sukeerthi teja Rallapalli wrote: > Jen, > > Thank you so much. In the NGS toolbox what option should i choose. > > Regards > Teja -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

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finding Conserved non coding region
by De Kumar, Bony 16 May '11

16 May '11

Hi all , I have a set of 1500 sequence obtained from my Chip_Seq experiment. I am interested to Know how many of them are within Conserved non coding Region. My definition of conserved Non coding region is as follows 1. Atleast a 200bp region with 80% conservation between Human , Mice and Chicken 2. Atleast a 200bp region with 70% conservation between Human , Mice , Chicken and Fish If someone can suggest me how to use galaxy for this purpose. Thanks in advance. Bony

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Phylogenetic tree viewer ?
by Luobin Yang 16 May '11

16 May '11

Hi, Do you guys know any phylogenetics tree viewer that works well with Galaxy system? Thanks, Luobin

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SNP annotation
by Oliver, Gavin 12 May '11

12 May '11

Hi, I am new to Galaxy and am wondering what tools are available for annotation of SNPs? I know that snpEff is implemented in Galaxy and this enables annotation such as location and predicted effect, however I am wondering if there are any automated means of annotating a polymorphism as known/novel or determining its frequency in the population. Does Galaxy offer anything like this or would it be necessary to create scripts that would for exampole compare to dbSNP for uniqueness and the 1000 genomes project for frequency. Best, Gavin The contents of this message and any attachments to it are confidential and may be legally privileged. If you have received this message in error, you should delete it from your system immediately and advise the sender. Almac Group (UK) Limited, registered no. NI061368. Almac Sciences Limited, registered no. NI041550. Almac Discovery Limited, registered no. NI046249. Almac Pharma Services Limited, registered no. NI045055. Almac Clinical Services Limited, registered no. NI041905. Almac Clinical Technologies Limited, registered no. NI061202. Almac Diagnostics Limited, registered no. NI043067. All preceding companies are registered in Northern Ireland with a registered office address of Almac House, 20 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK. Almac Sciences (Scotland) Limited, registered in Scotland no. SC154034. Almac Clinical Services LLC, Almac Clinical Technologies LLC, Almac Diagnostics LLC, Almac Pharma Services LLC and Almac Sciences LLC are Delaware limited liability companies and Almac Group Incorporated is a Delaware Corporation. More information on the Almac Group can be found on the Almac website: www.almacgroup.com

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Stastistics _q valu
by vasu punj 12 May '11

12 May '11

I am trying to use stat function of Galaxy, and compute q value from p values. it is giving following errors: An error occurred running this job: Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : scan() expected 'a real', got 'pvals' Execution halted Any suggestion

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Re: [galaxy-user] Galaxy Help: Extract sequences from [gtf file] + [genome FASTA file]
by Jeremy Goecks 12 May '11

12 May '11

Edge, Please send questions like this to the galaxy-user mailing list, where many people see your email and can help you and/or benefit from it. I've cc'd the list for this reply. The thread you linked to is out of date. To get sequences for the features in a GTF file, you can use the 'Extract Genomic DNA' tool and set the option 'Interpret features when possible' to Yes. To get sequences for Cufflinks transcripts, use the transcripts.gtf as input to the tool. Best, J. On May 12, 2011, at 3:08 AM, Edge Edge wrote: > > I just read through the post at the following link, http://lists.bx.psu.edu/pipermail/galaxy-user/2011-February/001934.html > I'm facing the same problem as well. > I'm desired to extract out the assembled transcript by Cufflink. > Can I know that how I link my output file from Tophat and Cufflink with the Galaxy? > I'm having the following output file right now: > junctions.bed > insertions.bed > deletions.bed > accepted_hits.bam > human_reference_genome.fasta > transcripts.gtf > isoforms.fpkm_tracking > genes.fpkm_tracking > > Sorry that I got a bit confusing about the explanation that you given to Karen, "in order to get the sequence data for transcripts in a Cuff* GTF file, you'll want to select for only exons (use Galaxy's 'Extract Features' tool) and then use the resultant dataset as input to Extract." > > Thanks a lot for your advice. > > best regards > edge > Master Student > UTAR Malaysia

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Re: [galaxy-user] Extract sequences from [gtf file] + [genome FASTA file]
by Edge Edge 12 May '11

12 May '11

Hi, I just read through the post at the following link, http://lists.bx.psu.edu/pipermail/galaxy-user/2011-February/001934.html I'm facing the same problem as well. I'm desired to extract out the assembled transcript by Cufflink. Can I know that how I link my output file from Tophat and Cufflink with the Galaxy? I'm having the following output file right now: junctions.bed insertions.bed deletions.bed accepted_hits.bam human_reference_genome.fasta transcripts.gtf isoforms.fpkm_tracking genes.fpkm_tracking I got a bit confusing about the explanation below: " in order to get the sequence data for transcripts in a Cuff* GTF file, you'll want to select for only exons (use Galaxy's 'Extract Features' tool) and then use the resultant dataset as input to Extract." Thanks a lot for advice. best regards edge

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