Hi, I met a problem when I use rnaSPAdes. After transcriptome assembly with rnaSPAdes, how to generate the unigene.fasta file? Since I need to prepare a two-column map file of transcript-to-gene-ID for downstream salmon analysis. Most of experiments described in the published articles use Trinity as the assembler and unigene.fasta files can be obtained with the script in Trinity, but it doesn’t work for rnaSPAdes.
I notice that a description in rnaSPAdes documentation:
" Each contig has the following id format: NODE_97_length_6237_cov_11.9819_g8_i2, where g8 means gene number 8, and i2 means isoform number 2 within this gene." Does this mean that “NODE_97_length_6237_cov_11.9819_g8” is the gene id, while “NODE_97_length_6237_cov_11.9819_g8_i2” is the transcript id? Is the largest number following the "g” is the number of transcripts that rnaSPAdes assembled?
Hi @luweidong
Your guesses are on the right track. Please see the help here for more details: https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_differential_expression_help.html