act comparaison of 2 genomes - problem with the blast output

Question

[lagartija]

Hello,

I don't know if any of you came across that problem before but when I do a blast of one genome against a database (with the 2nd genome) I get a blast against only one of the contigs in the output. I am not sure whether the blast didn't work or if I just have to change the ACT display. I tried megablast and blastn as tasks with the same result. I know this result can't be because the genomes I am comparing is the draft vs the final assembly so there should be blast hits all the way.

Thank you very much in advance, Cheers

[Bastien Hervé]

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I do a blast of one genome against a database (with the 2nd genome) I get a blast against only one of the contigs in the output

So as I understand, you did a database with contigs from a second genome. This second genome is your draft or your final assembly ?

How long are your genomes ? Maybe blast is not the best tool to use with full genomes

[Bastien Hervé]

Did you check the blast output ? Is there only hits with the same contigs ?

[WB]

hello i'm having the exact same problem you had. Have you been able to resolve this error? Thank you so much

Answer 1

[lagartija]

Exactly. The genome is not that big (7.2M) Normally it should be the right tool to use as ACT works with a blast as input file. Then there is also the online blast tool for that but it seems that it's not in use anymore...