Hello all,
I am trying to determine the percentage of reads in my sample mapping to ribosomal rRNA sequences. Unfortunately the Rhesus macaque .gtf I am using is not annotating for rRNAs or other small non-coding RNAs. To get around this, I indexed a small .fasta file I compiled containing 18S rRNA sequences from rhesus macaques. For this particular run, I did not include an annotation file. I am simply interested in reads mapping to my small .fasta reference. When I try to align to the indexed .fasta:
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/hpcdata/lmm/lmm_data/muddjc/STAR-2.5.2b/bin/Linux_x86_64/STAR --genomeDir /hpcdata/lmm/lmm_data/muddjc/18S_index --readFilesIn <.fastq> --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --outFilterMultimapNmax 1 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0 --outFilterMismatchNmax 2 --outFileNamePrefix /hpcdata/lmm/lmm_data/muddjc/JB37_18S_test
Nov 02 15:19:23 ..... started STAR run
Nov 02 15:19:23 ..... loading genome
Transcriptome.cpp:51:Transcriptome: exiting because of *INPUT FILE* error: could not open input file /hpcdata/lmm/lmm_data/muddjc/18S_index/exonGeTrInfo.tab
Solution: check that the file exists and you have read permission for this file
SOLUTION: utilize --sjdbGTFfile /path/to/annotantions.gtf option at the genome generation step or mapping step
Nov 02 15:19:24 ...... FATAL ERROR, exiting
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It seems that STAR is wanting an annotation file for the alignment. I think because no gtf is provided in the index step, it's not generating the "exonGeTrinfo.tab". Is it possible to run the alignment without a .gtf and how might I modify my command to accomplish this?
Thanks so much.
jc