Hello Elad, It would be best to start with the "Convert Formats -> SFF converter" tool. It can create FASTQ or FASTA + FASTA quality file output, depending on which downstream tool you prefer. Please give this a try and let us know if we can help again, Best, Jen Galaxy team On 2/28/12 11:17 AM, Elad Firnberg wrote:
Hi,
I am starting off with 454 read data in an sff file. I would like to get quality statistics on the data, but having trouble getting the tools to work.
I first tried to convert to a fastq file and use the "Compute Quality Statistics" tool, but I get this error, "An error occurred running this job:/fastx_quality_stats: found invalid nucleotide sequence "/ I then tried the "fastq groomer" and repeated the "Compute Quality Statistics", but got the same error. Perhaps it cannot handle the longer 454 sequences? / / Alternatively I tried converting the sff file to a fasta file and quality file. I had to manually convert the quality data file to qual454 for the "Build Base Quality Distribution" tool to recognize it, but upon doing that I got this error: /"/An error occurred setting the metadata for this dataset." And the Build Base Quality Distribution tool, also failed. / / / / Any help resolving this issue would be appreciated, Thank you, Elad
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support