%22safe%22%20mRNA%20fragments%2C%20first%2C%20second%20and%20third%20batch

"safe" mRNA fragments from first batch satisfy
1) minimum length of 500bp
2) has 100% cDNA coverage (at least 1-fold)
3) agrees 100% with gene from OGS
4) at least 50Kb apart from all other "safe" mRNA fragments or separated by an EST terminus

"safe" mRNA fragments from second batch satisfy
1) minimum length of 500bp
2) has 100% cDNA coverage (at least 5-fold at each position)
3) agrees 100% with a gene from OGS or from AUGUSTUS
4) at least 3Kb apart from all other "safe" mRNA fragments or separated by an EST terminus
5) does not align to the same transcript contig as another "safe" fragment (to avoid knock down of same gene due to split gene mispredictions)

"safe" mRNA fragments from third batch satisfy
1) minimum length of 500bp
2) has 100% cDNA coverage (at least 5-fold at each position)
3) agrees 100% with a gene from OGS or from AUGUSTUS with RNA-Seq hints
4) at least 6Kb apart from all other "safe" mRNA fragments or separated by an EST terminus or on different strands
5) does not align to the same transcript contig as another "safe" fragment (to avoid knock down of same gene due to split gene mispredictions)