reomve rRNA in bowtie2

Question

[ysbaek]

I am trying to remove rRNA from my total RANseq reads before alignment. I download ncRNA sequences (fa file) and used a command of $$bowtie2-build -f ./Sorghum_bicolor.Sorghum_bicolor_v2.ncrna.fa bt2_ncRNA_base to obtain index files, then which made 6 index files (bt2_ncRNA_base in the below command is the general name of files). Then I am trying to run actual bowtie command, as following but seems not working. Would you mind to give some tips for me to correct my command? Thank you very much in advance.

$ bowtie2 -x ./{bt2_ncRNA_base} Sorghum_bicolor.Sorghum_bicolor_v2.ncrna.fa -U ~/rongma2/raw_59seq/results/trimmomatic/bicolor_87_C12_1_CGCTCATT-GTACTGAC_L00M_R1_001_trimmed.fastq -S ./seqdata.sam -un ./seqdata_removerRNA.fq

Answer 1

[h.mon]

Use SortMeRNA or BBDuk + ribokmers.fa.gz file do remove rRNA. Removing all ncRNA is more than you want, you may have interesting stuff there.

Please post the error bowtie2 returns, instead of "seems not working", which is not helpful at all.