[galaxy-user] Manipulate FASTQ question

Hi, I currently have read names with the format: @N57638:1:64JU0AAXX:1:1:1057:943 1:Y:0: and would like to change them to the format: @N57638:1:64JU0AAXX:1:1:1057:943/1 I use Manipulate FASTQ, on all reads and set 'Manipulate Reads on:' to 'Name/Identifier', ('String Translate' becomes the only

Re: [galaxy-user] version tophat and cufflinks

Hi Dongdong, The version of TopHat is 1.2.0 and Cufflinks is 1.0.1. The full list of all Galaxy dependencies can be found on the wiki at: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies All the best, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury

Re: [galaxy-user] Regarding .exe file

Shambhavi, Any tool that can be run from the command line, whether it be a .exe, .sh, .pl, .ph, etc, can be installed in Galaxy. All this is explained on the wiki. The best page to start would be: http://wiki.g2.bx.psu.edu/Admin/Tools Cheers, Graham Dr. Graham Etherington Bioinformatics Support

Re: [galaxy-user] 'Draw quality score Boxplot' error

Caroline, I've had this problem before and find that although the job 'fails', the boxplot is actually created. If you click on the 'eye' in the boxplot history item, you should still be able to see and save your plot. Regards, Graham Dr. Graham Etherington Bioinformatics Support Officer, The

Re: [galaxy-user] Chip-seq data

Giuseppe, Your ChipSeq data is already in fastq format. It appears to have Illunima quality scores, so you'll need to use the NGS:QC and manipulation FASTQ Groomer tool, using 'Illumina 1.3+' as input and 'Sanger' quality format as output. As to using MACS, I've never used it before but you

Re: [galaxy-user] extract genome sequence

Yan, One way to do this is to create an interval file with the new co-ordinates (+/- 5kb) and then use the Fetch Sequences Extract genomic DNA tool. To create a new co-ordinates file, input your annotation file into the Text Manipulation Compute tool, using expressions like c3 = c3-5000 to get

Re: [galaxy-user] History items remain pending (grey color)

Hi Priya, If you are using one of the public Galaxy servers (e.g. http://main.g2.bx.psu.edu/), then it's quite probable that there a lots of jobs queued in the system by other users. If your history item is grey that means the job has been successfully submitted and is waiting its turn in the

Re: [galaxy-user] Cuffdiff version not apparent

Hi Cory, A list of Galaxy dependancies can be found on the wiki at: http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies ...although many tools allow a range of tool versions. You can also identify the information about the specific tool versions by clicking on the View Details Œi¹ icon

[galaxy-user] Creating a Trackster visualisation from a reference in your history

Hi, I’m struggling to figure out how to visualise a SAM file in Trackster as a normal user (i.e. without admin privileges). I’ve tried both my local install and use galaxy.org. This is what I’ve done on usegalaxy.org: Uploaded paired-end fastq sequences and a reference fasta file. Mapped with

Re: [galaxy-user] Summary Statistics

Hi Dominique, I’d use the original fasta file and input it into the 'Fasta Manipulation Compute Sequence Length' tool Then, using the output, run the 'Statistics Summary Statistics for any numerical column' tool on c2. That will give you all the info you’re after. Cheers, Graham Dr. Graham