Introduction After a long gestation we’ll be releasing a new version of FastQC in the near future to address some of the common problems and confusions we’ve encountered in the current version. I’ll write more about this in future posts but wanted to start with the most common complaint, that the duplicate sequence plot was…
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A new way to look at duplication in FastQC v0.11
Choosing the best format for raw sequence data
Introduction In the current Illumina pipeline raw sequence data is generated in qseq files, but can optionally be converted to the more standard FastQ format for use with other analysis programs. The FastQ files produced are uncompressed text files and take up a considerable amount of space in our storage system. We’ve therefore been thinking…
Interpreting the duplicate sequence plot in FastQC
Background The one analysis module which seems to elicit more questions than any other is the duplicate sequence plot. Of all of the plots which the program generates it’s probably the one which causes the most warnings / errors in otherwise nice looking data. I’m happy to admit that it’s not always immediately obvious what…