May I know what is the difference between --input-format PairedEndFastqManifestPhred64 and --input-format PairedEndFastqManifestPhred33 and CasavaOneEightSingleLanePerSampleDirFmt, Is it about sequencing device that has been used for sequencing? I always use --input-format PairedEndFastqManifestPhred33 as default for my paired end seq reads, How I can make sure that the input format I use is correct ? I tried to find the answer on google but couldn’t find any useful information.
Thank you for your help. I really appreciate it.
The Phred variations are explained well here.
The difference between manifest format and casava format is explained in our importing tutorial, or at least the practical difference for you: Casava format files have a specific naming pattern, otherwise both are for demultiplexed fastq data.
Phred64 is an older variation of the fastq quality scores, so unless if you know you are using old data then Phred33 is probably correct.
Phred33 and Phred64 have quality scores on different scales, so chances are you will get an error message if you try importing in the wrong format! So if you are importing without issue, you probably picked the correct format.
I hope that helps!
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