MIRA de novo assembly with reference genome doubt

[chariko]

Hello everybody,

I recently downloaded Mira software and I am getting some doubts I hope someone can help me to resolve.

My experiment consists in a paired end Illumina de novo assembly having a similar reference genome. As explained in the Mira Manual, it is recommended to do first a mapping and afterwards when the mapping has ended, get the list with the not mapped reads and do a de novo assembly with them (taking them from the original fastq file).

As result I got 2 caf files, one with the results of the mapping and other one witih the results with the de novo assembly.

When loading this data to gap5 (first mapped reads and then importing the de novo caf results) it does not recognize the pairs comming from diferent files. I wonder if it is possible to join the 2 caf files before loading the data to gap5. I hope this will turn in pairs to be recognized.

Any other suggestion on how to proceed will be appreciated.

Thanks in advance,

[sklages]

You might want to ask this on the mira mailing list. It is likely that you obtain more help and/or solutions there ..

[chariko]

You are right, I got there the answer. Anyway the answer on how to join the caf files was as easy as:

cat file1.caf file2.caf >combined.caf

[sklages]

Maybe you should leave a pointer here to the mailing list answer for people to see what the solution of your problem was.