Uturn

Identifying DNA U-turn from whole-genome sequencing reads. The DNA U-turn is a special DNA structure that aligns across postivie and negative strands. This project mainly uses two-step mapping approach to find this structure in next generation sequencing data.

Prerequisition

The pipeline prerequisition includes bowtie2, gawk, cutadapt, seqkit, samtools, parallel and SE-MEI (extractSoftclippedRetain) in PATH.

Instructions of compiling SE-MEI

Download SE-MEI source code from Devon Ryan's repository. Make sure to include htslib submodule using --recursive

git clone --recursive https://github.com/dpryan79/SE-MEI.git

Change source code in extractSoftclipped.c to retain first alignmentment information in the output FASTQ header. The modified source code was named "extractSoftclippedRetain.c"

cp extractSoftclipped.c extractSoftclippedRetain.c

Editing line 22 in extractSoftclippedRetain.c as below, and save

 fprintf(of, "@%s|%s|%i|%"PRId32"|", bam_get_qname(b), hdr->target_name[b->core.tid], b->core.flag, b->core.pos+1);
 for(j=0; j<b->core.n_cigar; j++) {
   fprintf(of, "%i%c", bam_cigar_oplen(cigar[j]), BAM_CIGAR_STR[bam_cigar_op(cigar[j])]);
   }
 fprintf(of, "\n");

Change Makefile accordingly

  all: compactRepeats extractSoftclipped compareGroups extractSoftclippedRetain
  extractSoftclippedRetain: htslib extractSoftclippedRetain.o
	         $(CC) $(OPTS) $(INCLUDES) -o extractSoftclippedRetain extractSoftclippedRetain.o htslib/libhts.a -lz -lpthread -llzma -lbz2
  clean:
	       rm -f *.o compactRepeats extractSoftclipped compareGroups extractSoftclippedRetain

Make and make sure extractSoftclippedRetain runs smoothly, then add SE-MEI dir to your PATH

Run the pipeline

Drop the FASTQ files in the current directory and run

bash findUturn.sh

The pipeline will generate multiple output file. A brief description is listed below:

1. UR.txt is a space delimited file with three columns: read id, chrmosome:jump1-jump2, uturn type (left or right)
2. PR.txt is a space delimited file with two columns: read id, chrmosome:breakpoint1-breakpoint2
3. Uturn.profile is a space delimited file with two columns: chromosome:jump1-jump2, read count supporting the uturn event
4. Port.profile is a space delimited file with two columns: chromosome:breakpoint1-breakpoint2, read count supporting the porting event
5. Pattern.txt is a space delimited file with three columns: chromosome:jump1-jump2, read count of left uturn, read count of right uturn
6. ReadStart.txt is a space delimited file with four columns: read id, chromosome, readstart position on reference, reference strand of read start mapping to