[galaxy-user] samtools output
Hello, I am having trouble replicating the great output you get after running samtools "Filter pileup on coverage & snps with ten columns (with consensus)" when I try to run samtools locally on my computer. Unfortunately we are unable to use Galaxy with our new data as our files are too large to upload to the website. Do you use some other scripts in the back ground to get such an informative output? When I run the samtools commands samtools pileup -i -vcf RefSeq.fa aln_sorted.bam > aln_ivcf.pileup and then samtools.pl varFilter aln_ivcf.pileup | awk '($3=="*" && $6>=20 && $7>=20 && $8>=10)' > final_aln_ivcf.pileup I do not get useful information in the output that tells me how many reads are calling the alternative allele, & what the alternative allele is. Any help would be gratefully received. Thank you Alison Gardner ___ 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/
Re: [galaxy-user] samtools output
As an alternative, you can easily install Galaxy on your own computer to negate the upload time.. it's very easy if you have a *nix system: https://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy -K On Thu, Jul 7, 2011 at 11:12 PM, Alison Gardner wrote: > Hello, > > I am having trouble replicating the great output you get after running > samtools > "Filter pileup on coverage & snps with ten columns (with consensus)" when I > try > to run samtools locally on my computer. > > Unfortunately we are unable to use Galaxy with our new data as our files are > too > large to upload to the website. > > Do you use some other scripts in the back ground to get such an informative > output? > > When I run the samtools commands > > samtools pileup -i -vcf RefSeq.fa aln_sorted.bam > aln_ivcf.pileup > > and then > > samtools.pl varFilter aln_ivcf.pileup | awk '($3=="*" && $6>=20 && $7>=20 && > $8>=10)' > final_aln_ivcf.pileup > > I do not get useful information in the output that tells me how many reads are > calling the alternative allele, & what the alternative allele is. > > Any help would be gratefully received. > > Thank you > > Alison Gardner > > > > ___ > 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/ > ___ 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/
[galaxy-user] fastx toolkit on solid qual file
Hi all, I noticed Galaxy could parse qual file and output kinds of stats, which is said to be based on fastx toolkit. Yet fastx_quality_stats in fastx toolkit doesn't work on qual file of solid. Anyone has idea about the trick? Thanks. Xin Zheng ___ 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/
Re: [galaxy-user] fastx toolkit on solid qual file
Hello Zheng, In the Galaxy UI, the tool "NGS: QC and manipulation -> Convert SOLiD output to fastq" is to be used before running "Compute quality statistics for SOLiD data". You could also run this conversion tool command line, if that is how you are running fastx_quality_stats. Hopefully this helps, Best, Jen Galaxy team On 7/8/11 8:37 AM, Zheng, Xin (NIH) [C] wrote: Hi all, I noticed Galaxy could parse qual file and output kinds of stats, which is said to be based on fastx toolkit. Yet fastx_quality_stats in fastx toolkit doesn’t work on qual file of solid. Anyone has idea about the trick? Thanks. Xin Zheng ___ 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/ -- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org/ ___ 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/
[galaxy-user] Passing/Referencing arguments from XML to R script while using XML conditional tag
Hi, This may appear as a very basic question. I: I have in the past used "name" as the object that allows the argument reference to passed from XML to Rscript running in the background. However I am currently using a conditional tag that makes this slightly incomprehensible. My command line argument for Rscript is given in the tag. I have also tried to define Rscript reference by using XML filter tags "key" or "ref" but perhaps this is the wrong way to go. Argument $geoID is a text reference that that the user writes in. This ID is read into Rscript and within the script, I access the data using R package GEOquery. Argument $input_cel allows the user to upload a CEL file Argument $input_cel allows the user to upload a text tab limited file Codes are given below. The error I get on the galaxy interface is "NotFound: cannot find 'geoID'" xyz ppgalaxy.r $input $geoID $input_cel $input_exprs $platform $species $exptRecords_dist $exptRecords_consensus $exptRfingerprintTOconsensus $distHistogram GSM ID CEL file Upload Expression Vector Upload II. I call a param's tag within a param's, My codes are given below. The problem is, I should be able to read in three arguments (1) input_exprs : data file (2) platform name (3) selected Species. On the GUI, the platform and species is not visible Platform Input - GPL Get HOMO SAPIENS MUS MUSCULUS Any help or suggestion is much appreciated. Thanks Uma -- *Uma Saxena* ___ 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/
[galaxy-user] Galaxy Has a New Wiki
Hello all, It is my pleasure to announce that Galaxy has a new wiki: http://galaxyproject.org/wiki. This wiki contains all the content from the old bitbucket wiki, plus a bunch of new content (most of which is still work in progress). The new wiki is based on MoinMoin and includes several new or improved features: * Search! * an automatically generated list of all pages (click on All Pages in sidebar) * Ability to upload files and images without using Mercurial. * plus a lot more The content, organization, and look and feel haven't entirely settled yet, so expect things to move around for a bit. You don't need any special knowledge to read the wiki. If you want to update the wiki you'll need to create a login (click on the Login link). Anyone can create a login, but you will need to answer a random (but hopefully easy) question about Galaxy to do so*. You can use either MoinMoin markup or Creole markup (but not both on the same page). We are hoping that the new wiki will be both much easier to use and to update than the old one. If you have any questions or comments, please send them to me or to the list as appropriate. Look for more emails as more features in the wiki become fully functional. Thanks, Dave C. * And you will be asked to answer questions every time you update pages. If you get tired of this (and you will), please send me your wiki login and I will make those annoying (but spam-preventing) questions go away. -- http://getgalaxy.org http://usegalaxy.org/ http://galaxyproject.org/wiki ___ 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/
