Peak calling using spp package

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

• 2,177 views • link

updated 7.1 years ago by Devon Ryan

• written 7.1 years ago by chaudharyc61 •

1 answer

Fragment length, which is also known as template length.

• 0 views • link

written 7.1 years ago by Devon Ryan

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

• 0 views • link

written 7.1 years ago by chaudharyc61 •

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

• 0 views • link

written 7.1 years ago by Devon Ryan

More posts like this

handling bio replicates for chromHMM
written 2.2 years ago by Hasan_Daaboul •

Hello everyone! I am performing genomic states annotation using ChIP-seq bam files for different epigenomic markers experiments, each experiment has 2 biological replicates (2 bam …
How to interpret Per sequence GC content in FastQC for ChIP-seq data?
written 2.6 years ago by Logan •

Hello, I conducted QC using ChIP-seq data, and among the QC results, I observed that the GC distribution over all sequences in the 'Per sequence …
Plotting telomere to centromere data pf a genome
written 5.7 years ago by chaudharyc61 •

Hello everyone I am trying to plot my peaks (in case of ChIP-seq) and methylation data ( in case of BS-Seq) in a format of …
bowtie mate 2 error
written 6.1 years ago by Morris_Chair

Hello everyone, I'm working on ChIP-seq files and I'm getting this type of error > mem: invalid option -- '2' here is the code : …
error in reading bam file in methylKit
written 6.2 years ago by chaudharyc61 •

Hello everyone, I am working on methyl-seq data. I have used bismark for alignment and the alignment file is sorted and indexed BAM file. And …
ChIP-seq Input correlation
written 7.0 years ago by chaudharyc61 •

Hello Everyone I have done multiBamSummary on my ChIP-seq data, and i found that the data has correlation with my Input is 0.98 which is …
Handling replicates in Chip-seq
written 7.1 years ago by chaudharyc61 •

Hello everyone, I have three replicates for my ChIP-seq data, i did peak calling using MACS2, now i was thinking to get the common peaks …
Bedtools Intersect related
written 7.1 years ago by chaudharyc61 •

Hello everyone Let's say I have three files A.bed, B.bed and C.bed which are having coordinates of peaks. Using bed-tools intersect I got common peaks …
Error in peak calling using SPP package
written 7.2 years ago by chaudharyc61 •

Hello everyone I am using spp package for finding the peaks in my Chip-seq data Problem is in the package there's a function find.binding.positions(), in …
MACS2 - centering peaks
written 9.2 years ago by BioinfGuru

Hello all. I have been given vague instructions by my supervisor to check our ChIP-seq analysis pipeline on an example data set to see if …