The result of modifications.gff/csv using basemods_spark is not the same as the original pipeline in SMRT-Analysis v2.3.0

PengNi / basemods_spark

0 stars 0 forks source link

The result of modifications.gff/csv using basemods_spark is not the same as the original pipeline in SMRT-Analysis v2.3.0 #7

Open PengNi opened 6 years ago

PengNi commented 6 years ago

need to figure out why.

PengNi commented 6 years ago

It was bacause the -placeRepeatsRandomly option in blasr (the hitPolicy in pbalign).

Need to provide more options in the future. e.g.: pbalign hitPoligy=allbest/randombest

PengNi commented 6 years ago

It has been tested that when using allbest (in blasr and samFilter) with the data ecoli and yeast, the results of _basemodsspark and SMRT-Analysis are the same.

However, it will still be different between _basemodsspark and SMRT-Analysis in some repeat area because of our limitation in _basemodsspark for issue #6.