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dpwickland / GB-eaSy

Bioinformatics pipeline to process genotyping-by-sequencing (GBS) data
MIT License
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path to raw sequencer output #1

Open mictadlo opened 5 years ago

mictadlo commented 5 years ago

Hi, Is the following way correct to include multiple fastq files inside GB-eaSy_parameters.txt?

#path to raw sequencer output; LEAVE R2 BLANK IF SINGLE-END READS
RAW_READS_R1=/work/waterhouse_team/All_RawData/Benth/GBS/GBS_RNP1/10_S0_L001_R1_001.fastq
RAW_READS_R2=/work/waterhouse_team/All_RawData/Benth/GBS/GBS_RNP1/10_S0_L001_R2_001.fastq
RAW_READS_R1=/work/waterhouse_team/All_RawData/Benth/GBS/GBS_RNP1/10_S0_L001_R1_001.fastq
RAW_READS_R2=/work/waterhouse_team/All_RawData/Benth/GBS/GBS_RNP1/10_S0_L001_R2_001.fastq
...

Thank you in advance,

Michal

dpwickland commented 5 years ago

GB-eaSy can process only one GBS library at a time. The input to GB-eaSy is one GBS library (a GBS library usually consists of one file (or two, if paired sequencing) with reads from hundreds of multiplexed samples). GB-eaSy automatically demultiplexes the library into individual sample files.

So GB-eaSy input should not be individual sample files from that library and should not be multiple GBS libraries.