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--- evaluating_and_comparing_transcriptome_assemblies_with_rnaquast [2021/01/11 14:53] – cgeb2001
+++ evaluating_and_comparing_transcriptome_assemblies_with_rnaquast [2021/01/11 15:01] (current) – cgeb2001
@@ Line 1: / Line 1: @@
 ===== Evaluating and comparing transcriptome assemblies with rnaQUAST =====
+Documentation by Joran Martijn (11 January 2021)
 Once you have assembled your RNA-seq reads into transcriptomes, you'll want to have some sense of assembly quality, or just a summary of your transcriptome in general (number of transcripts, number of predicted genes, estimated completeness, longest transcript etc.)
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 Quick explanation on the options:
 <code>
--o            output_directory
+-o                  output_directory
--c            transcriptome1.fasta transcriptome2.fasta ... transcriptomeN.fasta
+-c                  transcriptome1.fasta transcriptome2.fasta ... transcriptomeN.fasta
--t            number_of_threads
+-t                  number_of_threads
--l            transcriptome_label1 transcriptome_label2 ... transcriptome_labelN
+-l                  transcriptome_label1 transcriptome_label2 ... transcriptome_labelN
--ss           invoke if you used a strand specific mRNA library
+-ss                 invoke if you used a strand specific mRNA library
---gene_mark   to activate gene prediction with GeneMark
+--gene_mark         to activate gene prediction with GeneMark
---busco       to activate completeness evaluation with BUSCO
+--busco <busco_db>  to activate completeness evaluation with BUSCO
 </code>