Tools for analysis of restriction enzyme cutting sites

Genome Cutter

Used for creating a list of all restriction site positions in human genome.

Used restriction enzymes and their consensus sequences:

- AluI    AGCT                                         
- SaqAI   TTAA 
- MvaI    CCWGG (where W is A or T)
- HinfI   GANTC (where N can be any nucleotide)

Usage

$ perl genome-cutter.pl /path/to/chr/fasta/files/

Input

chromosome sequence file in FASTA format

Output

chr  start  end  enzyme  motif
Chr5	11895	11898	SaqAI	TTAA
Chr5	12072	12076	HinfI	gattc
Chr5	12287	12290	AluI	agct
Chr5	12306	12310	MvaI	cctgg

Count Intersections

Pipeline for finding theoretical fragment sizes.

Usage

# extract only mapped reads
$ samtools view -b -F 4 aligned_reads.bam > mapped_reads.bam

# convert bam to bed format
$ bedtools bamtobed -i mapped_reads.bam > mapped_reads.bed

# find intersections of all ChromHMM regions and mapped reads
$ bedtools coverage -b K562_ChromHMM.bed -a mapped_reads.bed > reads_list.txt

# count the results for each 15 ChromHMM regions in 1kbp window
$ perl count-read-region-intersect-averages.pl reads_list.txt | sort -k1n > results.txt

Output

1_Active_Promoter   246.54
2_Weak_Promoter      77.24
3_Poised_Promoter    99.23
4_Strong_Enhancer   116.66
5_Strong_Enhancer    55.50
6_Weak_Enhancer      52.38
7_Weak_Enhancer      48.25

Citation

Org et al. (2019) Genome-wide histone modification profiling of inner cell mass and trophectoderm of bovine blastocysts by RAT-ChIP