bwa aln bank/eukaryotic-tRNAs.fa 3_redundancy/ALL.matrix.filter.tfa | bwa samse bank/eukaryotic-tRNAs.fa - 3_redundancy/ALL.matrix.filter.tfa | samtools view -bS - | samtools sort - 4_annotation/eukaryotic-tRNAs.fa.sort
bwa aln bank/hairpin_T.fa 3_redundancy/ALL.matrix.filter.tfa | bwa samse bank/hairpin_T.fa - 3_redundancy/ALL.matrix.filter.tfa | samtools view -bS - | samtools sort - 4_annotation/hairpin_T.fa.sort
bwa aln bank/LSURef_108_tax_silva_trunc.fasta 3_redundancy/ALL.matrix.filter.tfa | bwa samse bank/LSURef_108_tax_silva_trunc.fasta - 3_redundancy/ALL.matrix.filter.tfa | samtools view -bS - | samtools sort - 4_annotation/LSURef_108_tax_silva_trunc.fasta.sort
bwa aln bank/Rfam_T.fasta 3_redundancy/ALL.matrix.filter.tfa | bwa samse bank/Rfam_T.fasta - 3_redundancy/ALL.matrix.filter.tfa | samtools view -bS - | samtools sort - 4_annotation/Rfam_T.fasta.sort
bwa aln bank/SSURef_108_tax_silva_trunc.fasta 3_redundancy/ALL.matrix.filter.tfa | bwa samse bank/SSURef_108_tax_silva_trunc.fasta - 3_redundancy/ALL.matrix.filter.tfa | samtools view -bS - | samtools sort - 4_annotation/SSURef_108_tax_silva_trunc.fasta.sort