I am using Deconseq to remove human sequences from fastq files generated by Myseq Illumina. I created the database with the human sequences using:
bwa64 index -p hs_ref_GRCh38_p2 -a bwtsw hs_ref_GRCh38_p2_split_PS.fa.fasta > bwa.log 2 >&1
but now I don't know how to remove these sequences from my actual paired files, let's call them myfile_1.fq and myfile_2.fq
could you give some hints?