align_and_estimate_abundance error Trinty
Hello, I am trying to prepare a reference for alignment and abundance estimation.
I have taken the transcriptome fasta file, do I need to use genomic fasta file or gtf file?
I don’t understand this point. pl guide me
I am using this code
perl /cabinfs/opt/applications/trinity/trinityrnaseq-Trinity-v2.5.1/util/align_and_estimate_abundance.pl
–transcripts /cabinfs/home/princy889/cucumber/trim/trinity_out_dir/Trinity.fasta
–est_method RSEM –aln_method bowtie2 –trinity_mode
–prep_reference /cabinfs/home/princy889/cucumber/trim/GCF_000004075.3_Cucumber_9930_V3_rna.fa
error is
Error, don’t understand arguments: /cabinfs/home/princy889/cucumber/trim/GCF_000004075.3_Cucumber_9930_V3_rna.fa at /cabinfs/opt/applications/trinity/trinityrnaseq-Trinity-v2.5.1/util/align_and_estimate_abundance.pl line 293.
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