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WGLab / LongGF

A computational algorithm and software tool for fast and accurate detection of gene fusion by long-read transcriptome sequencing
GNU General Public License v3.0
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pacbio read pre-processing #16

Open gr8ape opened 2 years ago

gr8ape commented 2 years ago

Hi, Do you recommend using the pacbio reads that have been polished with CCS or is their benefit to using the raw subreads.bam file as input?

liuqianhn commented 2 years ago

Hi @gr8ape sorry for the late reply. In our previous evaluation several years ago, we found that RepeatHMM performs better on raw subreads and CCS reads induces larger estimation error. Feel free to share your evaluation to see whether PacBio improve CCS for repeat estimation recently.

gr8ape commented 2 years ago

Hi @liuqianhn , thanks for you reply. This is helpful to know. We're evaluating some fusion detection algorithms on long-read data currently and I will try to update when we have sufficient results to share