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


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