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

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PengNi opened this issue Nov 24, 2017 · 2 comments
Open

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

PengNi opened this issue Nov 24, 2017 · 2 comments

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@PengNi
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PengNi commented Nov 24, 2017

need to figure out why.
@PengNi
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PengNi commented Dec 24, 2017

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
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PengNi commented May 7, 2018

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

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

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