Hello,
Sorry if there has been an answer to this elsewhere- i couldn't find it.
I've been given the task of extending some short ESTs with pieces of genome sequence that have been accumulated for a particularly AT-rich organism. There is no complete genome yet but my lab doesn't want to wait for the assembly-which may be six months down the line.
I've tried to align the ESTs to the genome contigs with cap3 but the assembly consistently fails to capture regions with introns properly.
I have tried to alter the -f,-r, and -h parameters but it's my first time trying cap3 and haven't gotten it right.
Can someone advise me about what are the correct parameters for this task?
thank you.
Sorry if there has been an answer to this elsewhere- i couldn't find it.
I've been given the task of extending some short ESTs with pieces of genome sequence that have been accumulated for a particularly AT-rich organism. There is no complete genome yet but my lab doesn't want to wait for the assembly-which may be six months down the line.
I've tried to align the ESTs to the genome contigs with cap3 but the assembly consistently fails to capture regions with introns properly.
I have tried to alter the -f,-r, and -h parameters but it's my first time trying cap3 and haven't gotten it right.
Can someone advise me about what are the correct parameters for this task?
thank you.
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