After Trinity assembler finished its assembly i managed to calculate the basic statistics of the assembly which are as below
File: Trinity.fasta Number: 158863 Total size: 176660784 Min size: 201 Max size: 22887 Average size: 1112.03 Median size: 665 N50: 1863 size @ 1Mbp: 11440 Number @ 1Mbp: 65 size @ 2Mbp: 8461 Number @ 2Mbp: 170 size @ 4Mbp: 7088 Number @ 4Mbp: 430 size @ 10Mbp: 5424 Number @ 10Mbp: 1417
Now my question is does these values look reasonable. Though N50 looks good i am worried about the number of transcripts that are less than 1kb (~ 60%) of the overall transcripts. Is this normal in Trinity?
Also how do people normally do downstream analysis after getting the assembly to select the best transcritps. I ask this because the number of Transcripts is way higher than expect number of genes in related species.