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a2iEditing / RNAEditingIndexer

A tool for the calculation of RNA-editing index for RNA seq data
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Confused about the MAPQ filtering #27

Open YiweiNiu opened 3 years ago

YiweiNiu commented 3 years ago

Hi,

Thank you for developing this useful tool.

I checked the log by RNAEditingIndexer and found a potential bug.

In "Step_5_strand2 - pileup", the samtools mpileup command did not output the MAPQ, which should include -s (--output-MQ).

But in "Step_7 - CountPileup strand 1 or 2", EditingIndexJavaUtils.jar PileupToCount need a parameter of -q (--qualityThreshold), which was given by parameter -f 33 in RNAEditingIndexer default setting.

Since the MAPQ was not written to the mpileup files, how the MAPQ filtering worked in RNAEditingIndexer?

Thanks, Yiwei