Custom contaminants_list

optimuscoprime / autoadapt

Automatic quality control for FASTQ sequencing files

GNU General Public License v2.0

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Custom contaminants_list #1

Open drmjc opened 10 years ago

drmjc commented 10 years ago

Hi optimuscoprime, fastqc 0.10.1 doesn't have the Illumina Nextera adaptor sequences in the contaminants file. But, it does have a --contaminants flag, which allows you to specify a custom contaminants txt file. It would be great if autoadapt accepted that param, and passed it on to fastqc.

optimuscoprime commented 10 years ago

Good idea. As a workaround for now, you could change the contaminants_list.txt file in the tools/install/fastqc folder to contain the sequences you are interested in