# make.fastq formats

**URL:** <https://forum.mothur.org/t/make-fastq-formats/2257>\
**Category:** Commands in mothur\
**Created:** [February 18, 2015, 9:58am UTC](https://forum.mothur.org/t/make-fastq-formats/2257 "2015-02-18T09:58:45Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![jenz](https://avatars.discourse-cdn.com/v4/letter/j/4bbf92/32.png) [@jenz](https://forum.mothur.org/u/jenz)\
**Post date:** [February 18, 2015, 9:58am UTC](https://forum.mothur.org/t/make-fastq-formats/2257/1 "2015-02-18T09:58:45Z")

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Hi,  
do I understand correctly that you just add the coding that you know your .qual file has as a format= parameter for make.fastq command.  
For example I have illumina 1.8 quality scores Ill put make.fastq(fasta=a,fa,qfile=a.qual, format=illumina1.8), if solexa then format=solexa.  
The format parameter is NOT to convert from one format to another etc?  
edit: a feature request - several programs and databases accept also space delimited decimal quality scires for fastq qaulity format. maybe add that format too

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**Author:** ![westcott](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/westcott/32/18_2.png) [@westcott](https://forum.mothur.org/u/westcott)\
**Post date:** [February 18, 2015, 2:35pm UTC](https://forum.mothur.org/t/make-fastq-formats/2257/2 "2015-02-18T14:35:03Z")

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You are correct the format parameter is used to tell mothur what format your fastq files are in. Mothur uses this information to properly translate the quality characters to scores.

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**Author:** ![jenz](https://avatars.discourse-cdn.com/v4/letter/j/4bbf92/32.png) [@jenz](https://forum.mothur.org/u/jenz)\
**Post date:** [February 26, 2015, 10:14am UTC](https://forum.mothur.org/t/make-fastq-formats/2257/3 "2015-02-26T10:14:59Z")

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So if I happen to have quality scores that are just pure Phred (an output from a bioinformatic program). Then should I convert them before using make.fast format=sange by shifting the values up by 33?.  
Using the default/sanger format: right now if I enter my values as they are then my Phred score of 40 will be convertedto I=(phred score of 72 sangfer score of 40) - which seems to be all-ready correct approach? If I’d pre-convert them they would be presented as too large?