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Can someone tell me how to go from a fastq file input for the runCA command to a .frg file. I know that fastqToCA produces a pointer to the original fastq file, but I am not sure how to use this on the command line with runCA. Any help is much appreciated. Thanks.
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I've used a script "convert-solexa-to-v2.pl" in wgs-assembler (ver 6.0b) package. Remember quality values are encoded in ASCII by adding 48 (ASCII zero) to the quality value in frg format. -
Oh, I did not see that binary. Ill try that and let you known if it works.Comment
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there is a convert-v1-to-v2.pl but not the one you mentioned.Comment
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