[galaxy-user] Galaxy toolshed-vcftools

Hi I was wondering if there is a wrapper already for vcftools in Galaxy. I want to use the following functionalities of vcftools but I haven't found it in toolshed. Thanks Mahtab Comparing vcf-compare A.vcf.gz B.vcf.gz C.vcf.gz Con

[galaxy-user] which reference genome should I select

Dear All, I am going to run Tophat with mouse RNA-seq datasets. When I uploaded the datasets with URL method, I chose "Mouse July 2007 (NCBI37/mm9) (mm9)" under Genome. So " database: mm9" appears in the brief description of each dataset in history. My question is: when I run Tophat, under "Wi

[galaxy-user] whixh setting should be used to upload mouse reference genome?

Dear All, I am going to search the alternative splicing events bentween datasets. I am not sure about the settings of mouse reference genome (mm9) when I upload it from UCSC Main. Would you please tell me the settings for 1) group: 2) Track: 3) Table: 4) Output format: Thanks. Jianguang

Re: [galaxy-user] which reference genome should I select

Hello, The option is "Use a built-in index" to use the mm9 reference genome database already in Galaxy (most likely what you want to do). Thanks, Jen Galaxy team On 8/14/12 8:31 AM, Du, Jianguang wrote: Dear All, I am going to run Tophat with mouse RNA-seq datasets. When I uploaded the dat

Re: [galaxy-user] whixh setting should be used to upload mouse reference genome?

Hello Jianguang, Please see "Basic Protocol 2: Loading Data and Understanding Datatypes" in this tutorial/publication: http://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012 The third dataset is the RefSeq genes dataset extracted from the UCSC Table browser. You could use this version

[galaxy-user] should I run FASTQ Groomer?

Dear All, I have some FASTQ datasets in phred 33 offset, and I have already assinged them Fastqsanger format. Do I need to run FASTQ Groomer on these datasets before I check the data quality by "Fastqc: Fastqc QC" and "FASTQ Trimmer by column" to remove bad nucleotides at 3' end of reads? Shou

Re: [galaxy-user] should I run FASTQ Groomer?

Hello Jianguang, Given this information, you will not need to run FASTQ Groomer, but simply proceed with Fastqc and FASTQ Trimmer. Best, Jen Galaxy team On 8/14/12 11:12 AM, Du, Jianguang wrote: Dear All, I have some FASTQ datasets in phred 33 offset, and I have already assinged them Fastq

Re: [galaxy-user] Map with Bowtie or Tophat?

Hello Irene, Both can be used with a custom reference genome - there is no difference between the tools in that regard. However, Bowtie is for mapping DNA and Tophat is for mapping RNA. More details are on the tool forms, including links to the primary tool home pages. Hopefully this helps,

[galaxy-user] how to sort mapped data?

Hi everyone, I am working on RNA-seq data. First, I mapped the reads to the reference transcriptome using bowtie. I found some different reads mapped to the same gene with different positions. Before running Cufflinks, I would like to combine the reads that mapped to the same gene though with

Re: [galaxy-user] mapping reads to an shRNA library?

Hello Suzie, There are two considerations: 1 - Will Bowtie allow very short sequence to be used as the reference genome? The answer appears to be yes, from the tool documentation. http://computing.bio.cam.ac.uk/local/doc/bowtie2.html#what-isnt-bowtie-2 It is certainly worth testing. Questions

Re: [galaxy-user] how to sort mapped data?

Hello Yan, To sort a SAM file produced by Bowtie before using it with Cufflinks (a requirement), please see this FAQ and workflow: http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq#faq2 Best, Jen Galaxy team On 8/14/12 7:33 PM, Yan He wrote: Hi everyone, I am working on RNA-

[galaxy-user] 答复: how to sort mapped data?

Hi Jen, Thanks for your reply! I know this workflow. I am just wondering if there is a tool in Galaxy to combine the reads that mapped to the same gene with different positions before running cufflinks. Thanks again, Yan -邮件原件- 发件人: Jennifer Jackson [mailto:j...@bx.psu.edu] 发送时间: We