Question: Peak calling using spp package
0
gravatar for chaudharyc61
5 weeks ago by
chaudharyc610 wrote:

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 ?

ADD COMMENTlink modified 5 weeks ago by Devon Ryan91k • written 5 weeks ago by chaudharyc610
1
gravatar for Devon Ryan
5 weeks ago by
Devon Ryan91k
Freiburg, Germany
Devon Ryan91k wrote:

Fragment length, which is also known as template length.

ADD COMMENTlink written 5 weeks ago by Devon Ryan91k

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

ADD REPLYlink written 5 weeks ago by chaudharyc610

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

ADD REPLYlink written 5 weeks ago by Devon Ryan91k
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