This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How can I tell my fastq is a fastqsanger or not?

Hi,

If I'm given a fastq file. How am I able to tell if it's a fastqsanger format or not? Is there a command line tool available for this? I really don't want to have to go into galaxy to ensure its format.

Thanks!

fastq fastqsanger
• 5,218 views • link
updated by GenoMax GenoMax • written by diltsjeri diltsjeri

A: Tool To Find Out If Fastq Is In Sanger Or Phred64 Encoding? head -n 40 file.fastq | awk '{if(NR%4==0) printf("%s",$0);}' | od -A n -t u1 | awk 'BEGIN{min=100;max=0;}{for(i=1;i<=NF;i++) {if($i>max) max=$i; if($i<min) min=$i;}}END{if(max<=74 && min<59) print "Phred+33"; else if(max>73 && min>=64) print "Phred+64"; else if(min>=59 && min<64 && max>73) print "Solexa+64"; else print "Unknown score encoding\!";}'

• 0 views • link
written by Medhat Medhat

Also, for clarification. Is it safe to assume that all the latest nexgen (NexSeq, HiSeq, IonTorrent, etc) technologies are outputting fastqsanger as the .fastq? Or should I just never assume anything?

• 0 views • link
written by diltsjeri diltsjeri

Assume it but make sure ;)

• 0 views • link
written by Medhat Medhat

2 answers

Thanks! Your google skills are better than mine.

• 0 views • link
written by diltsjeri diltsjeri

Use testformat.sh from BBMap suite.

• 0 views • link
written by GenoMax GenoMax

Log in to answer this question.

More posts like this