I used Trinity to make a de novo transcriptome assembly for 1 human sample (I will be using more samples later, this is just the test run). I want to assess the quality of the transcriptome. I've aligned the reads to the transcriptome using Bowtie and have an alignment of ~80%. Does 80% alignment imply that the transcriptome assembly was successful?
I wanted to also align my transcriptome (the Trinity.fasta output file) to the human reference genome, but the keep receiving errors related to the format of the Trinity.fasta file. Does anyone have any advice as to how to alter the Trinity.fasta file to make it compatible with Bowtie/Bowtie2? Or is there a different output file (in trinity_out_dir) that would be more appropriate?
I am very new at this - any help would be greatly appreciated! -Trish
If it is helpful, I have already run the TrinityStats.pl:
Counts of transcripts, etc. Total trinity 'genes': 109,215 Total trinity transcripts: 115,144 Percent GC: 45.72 Stats based on ALL transcript contigs: Contig N10: 2666 Contig N20: 1782 Contig N30: 1251 Contig N40: 883 Contig N50: 639 Median contig length: 321 Average contig: 518.17 Total assembled bases: 59,664,141 Stats based on ONLY LONGEST ISOFORM per 'GENE': Contig N10: 2366 Contig N20: 1548 Contig N30: 1082 Contig N40: 772 Contig N50: 570 Median contig length: 315 Average contig: 488.92 Total assembled bases: 53,397,469