Hello,
I am a first time Galaxy user.
I have uploaded my sequences as format “fastq” into Galaxy and would like to next use “Groomer” to output Sanger fastq format so to go on with exploring quality via box plot, deciding on a trim length (if any), and map to genome using bwa or bowtie.
However, I am running into a problem using “Groomer”.
I do not know what format my sequences are per setting the required input parameter.
An example of my sequences is as follows:
@SNPSTER6_0679:1:1:1083:939#0/1 run=100908_SNPSTER6_0679_70929AAXX
NATTTATGGATAGTTGGGTAGTAGGTGTAAATGTATGTGGTAAAAGGCCTAGGAGATTTGTTGATCCAATAAATATGATTAGGGAAACAA
+SNPSTER6_0679:1:1:1083:939#0/1
BIQQIQQQTP[[[[[VVVVQPPPPPTWWWW[[YYTTTOVV____TWVXRWPTQPQWWWWWTOOVV___V_TROOWTWTWTQWQWTTRWRO
… how to tell if you have: “Sanger”, “Solexa”, “Illumina 1.3+”, etc.
I have tried to submit to “Groomer” different times using these options one at a time and none return with results.
Need help please.
Also, what is the expected time for “Groomer” to return results for a file containing 2.7 million reads.
Thank you … best,
Kory
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Kory R. Johnson, MS, PhD
Sr. Bioinformatics Scientist
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Providing Contract Services For:
Bioinformatics Section,
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National Institutes of Health (NIH),
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