I was wondering if someone could help me? I am currently trying to do a step to check my ribosomal depletion step took during sequencing...using STAR Aligner. I had a plan to align the .fastq file to a ribosomal reference for homosapiens , and then write out a file that had all the unaligned reads (this would be the file I do my analysis on....it would not contain the rRNA contaminated reads)..then I planned to align that my Gh38 reference genome....however I keep getting an error and its not doing it...
Can someone help? I tried reading the manual and it is saying I must index first...I tried but I don't have a gtf file of my rRNA only Reference.
STAR --runThreadN 20 --genomeDir ~/directory/to my indexed/ribosomal/fasta/file --readFilesIn patient.fastq --outReadsUnmapped Fastx --genomeFastaFiles Hsapiens rRNA only reference file.fasta --sjdbOverhang max(ReadLength)-1
*Also does anyone know code to get it to give you only unmapped reads in a fastq file output?