Phantom Peak Quality Tools: Handling Negative Fragment Length
In a few edge cases, the estimated fragment lengths maybe < 0. This can be caused by a variety of factors such that are experimentally driven, such as poor ChIP efficiency (because of a bad antibody), or user driven, such as aligning to the wrong reference genome.
Issue:
We are using the first estimated fragment length for bigwig generation, i.e. comma separated strand cross-correlation peak(s) in decreasing order of correlation: -5,150,335.
Effects rule bam2bw in InitialChIPseqQC.snakefile
Solution:
Find the first non-negative fragment length for bigwig generation and other downstream uses. If all estimated fragement lengths are negative, choose the first negative value and include a comment in the resulting bash command: -5,-5,-5.
-e -5 # Negative value which will cause pipeline to fail (wrong ref genome selected or low starting DNA)
Phantom Peak Quality Tools: Handling Negative Fragment Length
In a few edge cases, the estimated fragment lengths maybe < 0. This can be caused by a variety of factors such that are experimentally driven, such as poor ChIP efficiency (because of a bad antibody), or user driven, such as aligning to the wrong reference genome.
Issue:
We are using the first estimated fragment length for bigwig generation, i.e. comma separated strand cross-correlation peak(s) in decreasing order of correlation:
-5,150,335.rule bam2bwin InitialChIPseqQC.snakefileSolution:
Find the first non-negative fragment length for bigwig generation and other downstream uses. If all estimated fragement lengths are negative, choose the first negative value and include a comment in the resulting bash command:
-5,-5,-5.-e -5 # Negative value which will cause pipeline to fail (wrong ref genome selected or low starting DNA)