I want to map de novo assembled transcript which is in full length (start codon to stop codon) to the draft genome and want to extract partially mapped or unmapped transcript.
I also want to discard chimeric transcripts.
Please help me to improve the gmap command line:
/home/software/gmap-2016-11-07/src/gmap -D /home/database -d Genome Trinity.fasta --chimera-margin=0 --min-trimmed-coverage=90 --min-identity=95 --failed-input /home/yog/failed.fasta
Will --chimera-margin=0 discard chimeric transcripts?
--min-trimmed-coverage=90 help to put all transcripts in failed.fasta which not able to cover 90% coding sequence of a gene?
--failed-input is these are the transcripts which do not completely map on genome according to above criteria?
**The genome which is I am using here is draft genome ...do not contain all the gene sequences and some of the gene sequences partially present in the draft genome.