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6 hours ago by

I have generated PASA gene structures to use them for gene training in SNAP, Augustus and other gene prediction software. However, SNAP produced errors for all the training genes identified on minus strand ("skipped due to errors"). It considered the genes on positive strand though. I am confused about this behaviour of SNAP. Did I made any mistake in file conversion? Following is the toy dataset:

 >ctg4
 Eterm   690335  690538  asmbl_142988.p1
 Exon    627558  627721  asmbl_142988.p1
 Exon    618407  618609  asmbl_142988.p1
 Exon    617865  617952  asmbl_142988.p1
 Exon    611927  611968  asmbl_142988.p1
 Exon    608393  608512  asmbl_142988.p1
 Exon    606645  606704  asmbl_142988.p1
 Exon    599937  600005  asmbl_142988.p1
 Exon    599526  599669  asmbl_142988.p1
 Exon    592777  592899  asmbl_142988.p1
 Exon    589983  590188  asmbl_142988.p1
 Exon    589422  589511  asmbl_142988.p1
 Einit   585167  586707  asmbl_142988.p1
 Einit   884878  885007  asmbl_143060.p1
 Exon    926290  926373  asmbl_143060.p1
 Exon    932048  932092  asmbl_143060.p1
 Exon    935718  935879  asmbl_143060.p1
 Exon    937104  937257  asmbl_143060.p1
 Eterm   938144  938274  asmbl_143060.p1

In the above example, the first gene is on minus strand, while the second gene is on plus strand.

Any comments on this issue will be highly appreciated.



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