Re: [galaxy-user] Stitch MAF blocks

2013-09-25 Thread Jennifer Di Tommaso
Hi, thanks for the answer. I understand my problem: I'm using mm10 and the alignment is avaible only for mm9, is it possible for you to fix it? Thanks. Jennifer Da: Jennifer Jackson j...@bx.psu.edu Inviato: marted? 24 settembre 2013 17:13 A: Jennifer Di

Re: [galaxy-user] Metagenomic filtering

2013-09-25 Thread Jing Yu
Hi Scott, My first thought is: 1. Remove rDNA sequences (and/or other well known highly-conserved sequences to reduce the workload in step 2). 2. Blast, then remove sequences with (say 99%) match to (say 5) genus. (Optional if step 1 is already good enough) For step 1: Build a fasta

Re: [galaxy-user] Stitch MAF blocks

2013-09-25 Thread Jennifer Jackson
Hello Jennifer, Yes, only hg19 and mm9 are locally cashed for the MAF tools. However, you can also load MAF data and use that from the history with these tools. The best way to do this is to load data by chromosome from UCSC: http://hgdownload.cse.ucsc.edu/goldenPath/mm10/multiz60way/ the /maf

[galaxy-user] generating pileup with max depth greater than 8000?

2013-09-25 Thread Lauren Oldfield
My question: How can I generate a pileup with an output of more than 8000 hits per base? I was generating pileups using the SAM tools -- Generate pileup and do not see an option to change the settings for output. In mpileup there is a variable that looks correct, -D (Output per-sample read

[galaxy-user] Trying to visualize 2 bam files from Galaxy

2013-09-25 Thread Ben Gift
I'm trying to start a visualizer with two different files to show a person where the variants are. Can I start IGV or something like it with multiple files? I read the docs and didn't find anything about it. I also asked here http://www.biostars.org/p/82032/

[galaxy-user] question

2013-09-25 Thread Bondici, Ibi
On the FastUnifrac webside available at the begining of the year I was able to obtain p-values having “unifrac_env.txt”file, GreenGene Core as the reference tree and “Automatically generate category mapping file” option was previously available. Can I have access to the previous

Re: [galaxy-user] question

2013-09-25 Thread Jennifer Jackson
Hello Vioricia, For this question, it would be best to contact the team that is hosting the public Galaxy site, as these are tools custom to their server. The contact information is on the bottom of the home page: http://unifrac.colorado.edu/ Best! Jen Galaxy team On 9/25/13 1:13 PM,

Re: [galaxy-user] Variant Annotation in GATK tools

2013-09-25 Thread Jennifer Jackson
Hi Yan, This is not enough information to give you a solution, but there are a few ways to investigate the problems or submit it to use for feedback. Is this error on the public Galaxy server at https://main.g2.bx.psu.edu (usegalaxy.org)? Of so, you can submit a bug report of the problem and