-mm paramater not working as expected

[martinclott]

When specifying a tag and setting 0 mismatches (the default) the software finds numerous reads with the tag. However, if we change the number of mismatches e.g. to 1 then no reads are found, we get the message 'None of the input files contained the specified tag'.

Our tag contains wildcard characters as reads start with a sequencing primer so our -t parameter starts with '.*.GG', I wonder if this is causing the issue and perhaps a more informative error message can be displayed if that's the case.

[lbarquist]

Hi Martin,

I've never tested the tag parameter with wildcards, and taking a quick look at the code I don't think it's set up to support this (though maybe @andrewjpage could comment?), and I'm not entirely sure how it would deal with these. From a skim of the code, I'm guessing not well, as you've seen.

My solution in the past to libraries where there are random bases incorporated in the tag has been to trim these off, so that I'm left with a determinate tag sequence -- is this possible in your case?

-Lars