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Old 10-31-2015, 02:16 AM   #1
krid
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Location: Germany

Join Date: Oct 2015
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Cool FASTA + FASTQ --> "FAST(q)" + FASTQ

I need some help out here with an actually not that difficult task and useful to my field of research. Unfortunatley I cannot find a tool which makes my whishes come true -> maybe you can help me out !

I have a fasta file and a fastq file.
The fasta file had been corrected. (fake fastq can be used)
The fastq data is raw uncorrected (with quality values of course).

the task would be to map the multi fastq file to the multi fasta file. After mapping adding only the quality values to the corrected multi FASTA file. Thereby merging a corrected FASTA and a uncorrected FASTQ.

FASTA + FASTQ --> "FAST(q)" + FASTQ

That is the theory - can help some out with the practical approach ?

Many thanks in advance
Krid
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Old 10-31-2015, 11:46 AM   #2
Brian Bushnell
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You may think this is not difficult, but actually, it is. For example, what do you intend to do with reads that map to multiple locations? Or reads that map with indels? Or reads that map with lots of substitutions?

Error-correction is very difficult and relies on assumptions of the error modes in the data needing correction. What kind of data do you have? Meaning library preparation, sequencing platform, etc.
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