Question

Peak calling using spp package

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5.5 years ago

chaudharyc61 ▴ 100

Hello everyone I'm using spp package for Chip-seq data so while reading the bam files, the data is showing three elements 1. tags, 2. flen and 3. quality What is flen ?

ChIP-Seq peak calling spp package • 1.6k views

ADD COMMENT • link updated 5.5 years ago by Devon Ryan 104k • written 5.5 years ago by chaudharyc61 ▴ 100

score 1 · Answer 1 · 2019-06-17

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5.5 years ago

Devon Ryan 104k

Fragment length, which is also known as template length.

ADD COMMENT • link 5.5 years ago by Devon Ryan 104k

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While calling peak it is creating problem I am using spp package for peak calling and it is not giving binding characterstics

ADD REPLY • link 5.5 years ago by chaudharyc61 ▴ 100

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SPP is relatively obscure, with few people outside of ENCODE ever using it. Try a more common peak caller like MACS2 or SICER.

ADD REPLY • link 5.5 years ago by Devon Ryan 104k