[maq-help] using MAQ on reads less than 20 bases long

[Joseph F. <jos...@gm...>]

Hi all,

maq chokes when I try to run it on reads less than 20 bp long ... I've got
some solexa data where the quality just drops right off after 10 cycles, but
there still should be some very useful data in the first 10 bases.  Is there
any way to force maq to accept these very short reads?  Any suggestions
would be appreciated.  Maybe I could pad with N's, or something similar?

Thanks in advance,
Joe
UC Davis Genome Center

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Joseph Fass
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