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

Question

[eimanpharmacist]

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!

[Pierre Lindenbaum]

Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they all work. If an answer was not really helpful or did not work, provide detailed feedback so others know not to use that answer.

• SortmeRNA command of the latest version does not work
• Prokka installation - compilation aborted
• fastq-dump - connection failed
• Add annotation_col in pheatmap
• Difference between DESEq2 and ANCOM for estimating biomarkers (which is preferrred?)