I recently assembled a number of transcriptomes using the Trinity pipeline. All proceeded smoothly until I began looking for isoforms. Most of the assemblies do not have any while a few have only a hand full (~5). All of the comp#s end in "_c0_seq1". My sequencing was not terribly deep; we multiplexed four individuals per lane of an illumina flow cell for RNAseq. Perhaps the sequencing was not deep enough to recover many isoforms?
I guess what I am asking is, how many isoforms should one expect from a Trinity assembly (e.g., 22,623 sequences in the Trinity.fasta output; average length of 610 nucleotides) sequenced in such a manner?
Thanks,
Michael
I guess what I am asking is, how many isoforms should one expect from a Trinity assembly (e.g., 22,623 sequences in the Trinity.fasta output; average length of 610 nucleotides) sequenced in such a manner?
Thanks,
Michael
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