Hello all, never done this before so i will need some guidelines. I am trying to do a de novo transcriptome assembly from a single rna-seq fastq file using Trinity (trimming makes a difference or no?). After 18h it produced a lot of files but i am guessing the one i want is the Trinity.fasta. After that i wanted to do annotation and blast. So i used TransDecoder ( https://github.com/TransDecoder/TransDecoder/wiki ),
TransDecoder.LongOrfs -t target_transcripts.fasta
TransDecoder.Predict -t target_transcripts.fasta
which i am guessing the target_transcripts.fasta is the Trinity.fasta ? and i got .pep, .cds, .gff3, and .bed files. Next step is :
util/gtf_genome_to_cdna_fasta.pl transcripts.gtf test.genome.fasta > transcripts.fasta
while i dont understand which file is the transcripts.gtf and the test.genome.fasta is which?