Question: Analysis 454 Quality Data
gravatar for Elad Firnberg
6.8 years ago by
Elad Firnberg20 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
ADD COMMENTlink modified 6.8 years ago by Jennifer Hillman Jackson25k • written 6.8 years ago by Elad Firnberg20
gravatar for Jennifer Hillman Jackson
6.8 years ago by
United States
Jennifer Hillman Jackson25k wrote:
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 -- Jennifer Jackson
ADD COMMENTlink written 6.8 years ago by Jennifer Hillman Jackson25k
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