How can I tell if it is from illumina 1.3 or 1.8 from fastq file?

Dear all,

I am going to use “Fastq manifest” formats to import my data. But I can’t know from the company that which one (illumina1.3 or illumina1.8) was used, can I tell from the fastq file? My data is like:

@M02419:285:000000000-B49GD:1:2106:22600:1714 2:N:0:ACTTGA
CGATGTGGACTACCGGGGTTTCTAATCCTGTTTGCTCCCCACGCTTTCGCGTCTCAGCGTCAGTTGTGTTCCAGTAAATCGCCTTCGCAATCGGTATTCCTTCTGATCTCTACGGATTTTACCCCTACACCAGAAATTCCATCTACCTCTCCCACACTCTAGGTATACAGTTTCAAAAGCAGTTCTATATTTAAGCTATAGGATTTCACTTCTGACTTATCTACCCGCCTAAACGCTCTTTACGCCCAGGTATTCCGAGTAACTCTTGCGTCCTCCGTATGACCACGGCTGCTGGCACGTC
+
CCCGGGGGGGGGGGGGGEGGFFFGGGGGGG9FGFFGGGGGGGGGGGGGGGCGGGGGGCEFGGGGGEFGGGGGGGFDEGFCFGEGGGGD:[email protected],E<,B,<?BFFG8FFCGCEEGGGGGEGGGE9EF,8DGEGGD,3DAD9BFFAE;;FF,@FFEECFFGGG9C9,,@,@[email protected]@=CC,:,=*@D?5);A4)2:5:+1C4=5E=F*)381:8E3)27>C++.94F3)7/34((,8,)-:2*-)451>?0)(-5<(##

Thanks for all the suggestions or idea!!!

Hi @Lennon_Lee - chances are you have Phred33 offset data, assuming it was sequenced within the last few years. I would import using the Phred33 variant that is appropriate for your data (single or paired). Once imported, run the demux summarize visualization and take a look at the quality scores histogram - that visualization will warn you if it identifies quality scores outside of the the Phred33 range. Hope that helps! :t_rex: :qiime2:

Thank you very much for your kindly help!!!

1 Like

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.