Hello. I am new to RNA seq. I assembled a transcriptome via Trinity. I would now like to assess the quality of my transcriptome.
I tried this string of commands using RSEM-EVAL:
npetrill@trogdor rsem-eval]$ ./rsem-eval-calculate-score --paired-end R1V22_B9F8St_ACTTGA_L002_R1_001.qualitytrimmer30.fastq R1V22_B9F8St_ACTTGA_L002_R2_001.qualitytrimmer30.fastq Trinity.fasta /home/richardsonlab/AMMA_transcripts/trinity_out_dir/rsem_eval_1.fa 100 rsem-synthesis-reference-transcripts /home/richardsonlab/AMMA_transcripts/trinity_out_dir/rsem_eval_1.fa.temp/rsem_eval_1.fa 0 0 0 Trinity.fasta rsem-synthesis-reference-transcripts : No such file or directory!
Please check if you have compiled the associated codes by typing related "make" commands and/or made related executables ready to use.
I am not sure what to make of this error message.Any help on what the next steps should be would be much appreciated.