Originally posted by habm
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For each of your paired library, analyze the file PREFIX.LibraryX.txt.
For example, for LibraryNumber 3:
less PREFIX.Library3.txt
And locate your peak near 6300 to find the real value. Let us suppose that it is 6189.
The column in these Library files are: observed outer distance and frequency.
Basically, you want to locate the observed outer distance with the maximum frequency near 6300.
Do that for all your paired libraries.
Then, edit your Ray command to include manually the average and standard deviation for each of your library:
mpirun -np 999999 /software/ray-version/Ray \
-p lib3_1.fastq lib3_2.fastq 6189 618 (replace 6189 by what you found in the Library file and let the standard deviation be around 10 %).
-p ...
Doing so will allow you to use the long-insert, but will ignore the paired information for the short-insert (within each library) because they won't be within the specified ranges.
Still, all the reads will contribute to building the genome graph.
Hope it helps.
Sébastien
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