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How to split the aligned output from SortMeRNA into forward and reverse sequences

Hi,

I ran this code to filter rRNA using SortMeRNA:

 sortmerna -ref ~/Documents/path/sortmerna/rRNA_databases_v4/smr_v4.3_default_db.fasta -reads ~/Documents/path/sortmerna/sequences/B_rRNA_F_2.fastq -reads ~/Documents/path/sortmerna/sequences/B_rRNA_R_1.fastq --workdir ~/Documents/path/sortmerna/working_dir2 --fastx fastq --paired_in --log -threads 3 --blast 1 --num_alignments 1 -v

I wonder how could I split the aligned output fq file into forward and reverse sequences to proceed into Qiime2?

Thanks!

metatranscriptomic sortmerna
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by eimanpharmacist • eimanpharmacist

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written by Pierre Lindenbaum Pierre Lindenbaum

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