PIDFE, P-element Insertion Detector and Frequency Estimator, is a pipeline to detect P-element insertions and estimate their insertion frequencies from paired-end reads.
Copyright (c) 2019 Kelleher Lab at the University of Houston. If you used PIDFE in your study, please cite: Zhang S, Pointer B, Kelleher E. 2020. Rapid evolution of piRNA-mediated silencing of an invading transposable element was driven by abundant de novo mutations. Genome Res. 30: 566-575
Current version v2.0
PIDFE identifies P-element insertions by detecting the split reads (read-1 in above figure), one part of which is mapped to P-element and the remaining part is mapped to the reference genome.
The following codes install PIDFE in home directory. Users can install it anywhere they want by changing '~' to their desired directory.
cd ~
git clone https://github.com/szhang32/PIDFE.git
chmod 755 -R ~/PIDFE/scripts
echo 'export PATH=$PATH:~/PIDFE/scripts' >> ~/.bash_profile
PIDFE is designed to run on a high performance computering platform with Linux operating system. The following softwares or packages are required to run PIDFE.
sh PIDFE.sh [-i inDir] [-o output] <-g refGenome> <-p refP>
Required arguments:
<-g refGenome> defines the reference genome where P-elements reside.
<-p refP> defines the consensus P-element sequence.
Optional arguments:
[-i inDir] is the directory containing paired-end read, i.e., *_R1.fastq and *_R2.fastq. Asterisk(*) can represent zero or any number of characters. Default: current working directoary
[-o output] is the output file name. Default: p_insertions.txt
The output file contains identified P-element insertion (1st column), the number of reads supporting each insertion (2nd column), and estimated frequencies (3rd column). Here is an example:
| insertion | supporting_reads | frequency |
|---|---|---|
| chr2L:12822166:+ | 27 | 0.844 |
| chr2L:20311155:- | 38 | 1 |
| chr2L:3632292:+ | 9 | 0.4285 |
| chr2L:3632292:- | 13 | 0.52 |
For each insertion, the inserted chromosome, insertion breakpoint, and orientation of the insertion are reported. For example, "chr2L:12822166:+" indicates that there is a sense P-element insertion at chromosome 2L at genomic coordinate 12822166. Sense ('+') represents the P-element insertion is in the same orientation as the plus reference genomic strand, whereas antisense ('-') represents the P-element insertion is in the same orientation as the minus reference genomic strand.
If you find any bugs or have difficulties using PIDFE, please feel free to contact Shuo Zhang (shuozhang23@gmail.com).