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The Illumina files come as compressed FASTQ files (`.fastq.gz` format) and there's two files per sample, corresponding to read 1 and read 2. +Your analysis starts with FASTQ files (if you need a reminder of what a FASTQ file is, look at the [Intro to NGS > FASTQ](03-intro_ngs.html#FASTQ_Files) section of the materials). The Illumina files come as compressed FASTQ files (`.fastq.gz` format) and there's two files per sample, corresponding to read 1 and read 2. This is indicated by the file name suffix: - `*_1.fastq.gz` for read 1 diff --git a/materials/30-poppunk.md b/materials/30-poppunk.md index fd11a41..79a5504 100644 --- a/materials/30-poppunk.md +++ b/materials/30-poppunk.md @@ -49,7 +49,7 @@ To run PopPUNK on our assemblies, the following commands can be used: mkdir -p results/poppunk # run PopPUNK -poppunk_assign --db GPS_v8_ref --external-clustering GPS_v8_external_clusters.csv --query qfile.txt --output results/poppunk --threads 8 +poppunk_assign --db GPS_v8_ref --external-clustering GPS_v8_external_clusters.csv --query assemblies.txt --output results/poppunk --threads 8 ``` The options we used are: