你好，我在 RNAseq-workflow中 about rnaseq-workflow

[ssyamoako]

Hello peiyu1223, i went to the analysis and i was able to overcome that.
i will help you here.

what you have to do is this below:
sortmernaREF=/home/waccbip/Desktop/new_workflow/sortmerna_db/rRNA_databases/rfam-5.8s-database-id98.fasta,/home/waccbip/Desktop/new_workflow/sortmerna_db/index/rfam-5.8s-database-id98:
/home/waccbip/Desktop/new_workflow/sortmerna_db/rRNA_databases/rfam-5s-database-id98.fasta,/home/waccbip/Desktop/new_workflow/sortmerna_db/index/rfam-5s-database-id98:
/home/waccbip/Desktop/new_workflow/sortmerna_db/rRNA_databases/silva-arc-16s-id95.fasta,/home/waccbip/Desktop/new_workflow/sortmerna_db/index/silva-arc-16s-id95:
/home/waccbip/Desktop/new_workflow/sortmerna_db/rRNA_databases/silva-arc-23s-id98.fasta,/home/waccbip/Desktop/new_workflow/sortmerna_db/index/silva-arc-23s-id98:
/home/waccbip/Desktop/new_workflow/sortmerna_db/rRNA_databases/silva-bac-16s-id90.fasta,/home/waccbip/Desktop/new_workflow/sortmerna_db/index/silva-bac-16s-id90:
/home/waccbip/Desktop/new_workflow/sortmerna_db/rRNA_databases/silva-bac-23s-id98.fasta,/home/waccbip/Desktop/new_workflow/sortmerna_db/index/silva-bac-23s-id98:
/home/waccbip/Desktop/new_workflow/sortmerna_db/rRNA_databases/silva-euk-18s-id95.fasta,/home/waccbip/Desktop/new_workflow/sortmerna_db/index/silva-euk-18s-id95:
/home/waccbip/Desktop/new_workflow/sortmerna_db/rRNA_databases/silva-euk-28s-id98.fasta,/home/waccbip/Desktop/new_workflow/sortmerna_db/index/silva-euk-28s-id98

#then after you index your database like this:
indexdb_rna --ref $sortmernaREF

then you run the final part of it this way:
for i in *_trimmed.fq;do
sortmerna
--ref $sortmernaREF
--reads $i
--aligned /home/waccbip/Desktop/new_workflow/results/3_rRNA/aligned/${i%.fq}_aligned.fq
--other /home/waccbip/Desktop/new_workflow/results/3_rRNA/filtered/${i%.fq}_filtered.fq
--fastx
-a 8
-v;done

I hope you follow the steps and get it fixed.

[bioinfotec]

The indexdb_rna binary has been removed from version 4.0.