Does it necessary to use both forward and reverse fastq input files in kmergnie?

Question

[nakandalau]

For kmergenie, I used the following command

kmergenie hiseq_reads_ecoli_R1.fastq -l 21 -k 121 -s 2 -o out_file.txt -t 16

But If I want to use both forward and reverse input files, how can I do that? I have tried importing the two files giving space in between them, but it doesn't work. Can you please tell me is it okay to use only one input file to choose the best kmer?

Answer 1

[liorglic]

In k-mer analyses (including KmerGenie), paired-end information is not used, so you can just use all your files - order doesn't matter. You have two options with KmerGenie:
1.Concatenate your fastq files:

cat hiseq_reads_ecoli_R1.fastq hiseq_reads_ecoli_R2.fastq > hiseq_reads_ecoli_R12.fastq
kmergenie hiseq_reads_ecoli_R12.fastq -l 21 -k 121 -s 2 -o out_file.txt -t 16

2.Use a reads list:

echo -e "hiseq_reads_ecoli_R1.fastq\nhiseq_reads_ecoli_R2.fastq" > reads.list
kmergenie reads.list -l 21 -k 121 -s 2 -o out_file.txt -t 16

Option 2 has the advantages that you don't need to duplicate your data and you can include as many files as you need.