Hi Can this tool available on Galaxy be used to sort a sam file before converting to bam file? Should the default settings be used for that or do i need to identify the columns? Thank you
Tool name: Sort
Tool version: 1.0.3
Tool ID: sort1
Hello,
Check out these published workflows for some ideas about how to use it. These sort in a way that is best for the RNA-seq tools in the Tuxedo suite (found on the public Main server http://usegalaxy.org) or MACS. But you can import and edit any way that you'd like. You can start with a SAM or BAM file, and preserve headers, as some of these do.
https://usegalaxy.org/u/jen-bx-galaxy-edu/w/sort-bam-inc-headers
https://usegalaxy.org/u/jen-bx-galaxy-edu/w/sort-bam-for-peak-calling-macs-tool
https://usegalaxy.org/u/jeremy/w/sort-sam-file-for-cufflinks
Hope this helps, Jen, Galaxy team
I have looked at these work flows and as far as i can see that using the alphabetical sorting of column 3 (RNAME) will place all the unmapped sequences with '*' at the top of the list.
Also won't chromosomes named 1, 3, 10, 11 be ordered 1, 10 , 11, 3?
Won't all of this cause problems for programs like 'Indel Realigner '.
Isn' there an easy way to go from a BWA>sam file to a sorted bam, using the tools on use https://usegalaxy.org/
Thanks Guy
Hello, The workflows are examples for RNA-seq pipelines. The Sort tool itself has many options for different types of sorting by fields. If you are not sure how each works, just run a small file through. For GATK, you will want to the sort order to be the same as the reference genome (which itself needs to be ordered "GATK style = 1,2,3,....X,Y,M"): try the tool "Picard: Reorder SAM/BAM". If you would like to review the latest set of tools we are building up (including more sorting tools) please see our test server: http://test.galaxyproject.org/ . The Tool Shed also has other sorting tools available for a local/cloud Galaxy: http://usegalaxy.org/toolshed
We really do test on the Test server, so if you run into a problem with a tool, sharing it as a bug report would be great. Just note that some tools are not fully set up on Test (this changes daily) and quotas are small - this is a server to experiment on.
Thanks, Jen, Galaxy team
Hi Jen
to get files onto http://test.galaxyproject.org/ is there way to transfer 1 or 2 easily from https://usegalaxy.org/ without having to FTP them?
Thanks
Thank you Bjoern and Jennifer for your input. to explain further, I needed to sort the bam file so that it could be used for a few of the picard analysis tools. IGV also requires sorted bam files. I was not sure if the sort tool on galaxy was the correct one to use since my data is already there. In the past I have used the sort command in IGVTools but I am not sure if that sorts by coordinates or reads.
Thanks again.
You can use "sort" for this, but you need to know exactly what you want to archive. Do you want to sort by coordinate or read name?