The inputs of TRUST

[yang]

Hi，Bo

      I admire your work. Whether quality control for raw RNA-seq  data is required  before getting bam file as input. If so, do I need to remove short reads on the step of  fastqc? 

Thanks,

[Bo Li]

Hi Yang,

I would recommend you to remove low quality reads before inputting to TRUST.

Thanks,

Bo

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[zhangda...@gmail.com]

Hi Bo,

         I mapping the paired-end RNA-seq reads using MapSplice, and got the bam file with more reads than the fastq file. Some reads have mapped to multiple locations on the genome. Should I keep all the hits or just one of them? As unmmapped read was located to the genome according to it's mate, the multi-mapped mate may introduce ambiguity.

Thanks,

Dan

在 2018年11月28日星期三 UTC+8下午10:30:52，Bo Li写道：

[Bo Li]

You don't need to worry about multiple mapping issue. It is taken care of in TRUST by setting a mapping quality threshold. You may directly apply TRUST to your bam file.

Thanks,

Bo

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[zhangda...@gmail.com]

So, generally speaking, at what kind of mapping quality threshold can you get rid of multiply mapping reads out? Do different mapping tools share the same strategy of measure mapping quality?

Thanks
在 2018年12月29日星期六 UTC+8上午2:24:11，Bo Li写道：