Does the number of paired reads have to be exactly the same in Platanus scaffolding?

Question

[gerrychang1985]

Greetings, everyone.

I've got an error feedback when assembling scaffold of a plant using platanus, it's listed below:

K=32, making hash table...
Error(2): File format exception!!
the number of read is different in paired-file.
K=32, making hash table...

As I filtered some of the low-quality reads, does the number of paired reads have to be exactly the same in Platanus scaffolding?

Thank you.

Answer 1

[george.ry]

I don't know specifically about Platanus, but the overwhelming majority of programs will expect the files containing each of the pairs to be the same length and to have reads appearing in the same order. That will almost certainly be your issue.