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Indexes and UMIs are incorrect in undetermined fastq and reports when having multiple libraries in the same run.
This does not affect the actual data for the reads that match with samples.

the current version of the mgikit trim the barcodes at the end of the reads after demultiplexing and attach the indexes and umis to the read header if the illumina format is requested.
It is better to have an option to keep the undetermined and ambiguous reads as they appear in the original data

Hi, I am having problems with demultiplexed files that were run without --disable-illumina option. Every now and then there is a wrongly parsed header that creates 5 lines in fastq file per read.

See the '@;H' header name with the actual name being on the next line.