[galaxy-user] inconsistent cuffdiff output

2012-08-20 Thread i b
Dear all, I have two samples, treated and untreated. I ran cufflinks and had the following: treated: 884532 untreat.: 130247 I then ran cuffdiff and look ath transcript diff. expression: treated: 33 untreat.:2.9 significant:yes Strangely for another transcripts I have: Cufflinks: treat_:0

[galaxy-user] inconsistent cuffdiff output-corrected question

2012-08-20 Thread i b
Dear all, I have two samples, treated and untreated. I ran cufflinks and had the following FPKM: treated: 884532 untreat.: 130247 I then ran cuffdiff and look at the transcript diff. expression values: treated: 33 untreat.:2.9 significant:yes Strangely for another transcripts I have the

Re: [galaxy-user] From gff to gff3?

2012-08-20 Thread Jennifer Jackson
Hi Yan, To see the tools available to work with GFF and GTF datafiles, please see the tool group Filter and Sort. Galaxy does not have a GFF-GFF3 converter - and I do not know of one. There is a GTF-GFF3 converter in the Tool Shed (details below). First, you will want to make sure that you

Re: [galaxy-user] Linking to Compressed Data

2012-08-20 Thread Jennifer Jackson
Hi Branden, Data in a library needs to be uncompressed in order for Galaxy to index and have access to it correctly. I updated our wiki for the upload by filesystem link option: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files Good question! Jen Galaxy team On

Re: [galaxy-user] Minimum length of read segments

2012-08-20 Thread Jennifer Jackson
Hello Jianguang, Unless you know that your genome has exons that are shorter in length than 25 bases long, then it is not necessary to modify this parameter. http://tophat.cbcb.umd.edu/manual.html -- How does TopHat find junctions? If shorter, then set the parameter to be that shortest

[galaxy-user] Table with gene count reads

2012-08-20 Thread Jennifer Jackson
Hello Mike, SAM datasets can be used as tabular data with the Text manipulation, Filter and Sort, Join, Subtract and Group, etc. if the headers are removed and the datatype changed. Or, you can convert the format to Interval. For the simplest count directly on the SAM/BAM format itself, the

Re: [galaxy-user] run Bowtie to estimate Mean Inner Distance between Mate Pairs

2012-08-20 Thread Jennifer Jackson
Hello Jianguang, On the Bowtie tool form itself, please find this text: Outputs The output is in SAM format, and has the following columns: Column Description 1 QNAME Query (pair) NAME 2 FLAG bitwise FLAG 3 RNAME

Re: [galaxy-user] Counting intervals in one file overlapping intervals in another file - what are the hidden settings?

2012-08-20 Thread Alex Shaw
Hi, I'm also interested in using bedtools with galaxy. I have found a bug. When I try to run Intersect multiple sorted BED files Error: The requested genome file (/galaxy/home/g2test/galaxy_test/tool-data/shared/ucsc/chrom/hg_g1k_v37.len) could not be opened. Exiting! I've used bedtools on the