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Important Note about the update:

**If your sequencing (paired-end) read length is >= 100 bases long and your sample was also enriched for circular DNA then it is recommended to use the following script ** "circle_finder-pipeline-bwa-mem-samblaster.sh"

**Note: If your sample was not enriched for circular DNA (like normal ATAC-seq, whole-genome sequencing, etc.) and read length >75 bases long then use the following script ** "circle_finder-pipeline-bwa-mem-samblaster.sh"

**Note: Circle_finder can not be used if your sample was not enriched for circular DNA before library preparation AND length of read <75.

#Usage: bash "Number of processors" "/path-of-whole-genome-file/hg38.fa" "fastq file 1" "fastq file 2" "minNonOverlap between two split reads" "Sample name" "genome build"

#bash /path-of-script-dirctory/microDNA-pipeline-bwa-mem-samblaster.sh 16 /path-of-script-dirctory/hg38.fa 1E_S1_L1-L4_R1_001.fastq.75bp-R1.fastq 1E_S1_L1-L4_R2_001.fastq.75bp-R2.fastq 10 1E hg38

#Arg1 = Number of processors

#Arg2 = Genome or index file "/hdata1/MICRODNA-HG38/hg38.fa"

#Arg3 = fastq file 1 "1E_S1_L1-L4_R1_001.fastq"

#Arg4 = fastq file 2 "1E_S1_L1-L4_R2_001.fastq"

#Arg5 = minNonOverlap between two split reads "10"

#Arg6 = Sample name "1E"

#Arg7 = genome build "hg38"

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Welcome to the Circle_finder wiki!

This is a step by step guide to run Circle_Finder (if your sample was enriched for circular DNA and the read length of your paired-end sequencing library is <75 bases).

Step 1: Clone the repository

git clone https://github.com/pk7zuva/Circle_finder.git

Step 2: Change to "Circle_finder" directory

cd Circle_finder

In this directory you will find four types of files: 1) *.c 2) *.sh 3) *.txt and 4) C executable that has no extension

Note: Though the "C" executable files are provided it is advisable to make these executable afresh

Step 3: Type the following command on your terminal one by one

cc -o ADDRESS2PROFILEPAIREND address2profile.pairend.c

cc -o DIRECT.REPEAT.FINDER1 direct.repeat.finder1.c

cc -o JUNCTIONAL.TAG junctional.tag.c

cc -o LEFT.ALIGNMENT left.alignment.c

cc -o MIDNA_START_END_SCORE midna_start_end_score.c

Step 4: Download the whole genome files and bowtie index files from link given in file "download-link-hg38-and-bowtie-index.txt"

cat download-link-hg38-and-bowtie-index.txt

http://genome.bioch.virginia.edu/CIRCLE_FINDER_MASTER/hg38.fa http://genome.bioch.virginia.edu/CIRCLE_FINDER_MASTER/hg38.1.bt2 http://genome.bioch.virginia.edu/CIRCLE_FINDER_MASTER/hg38.2.bt2 http://genome.bioch.virginia.edu/CIRCLE_FINDER_MASTER/hg38.3.bt2 http://genome.bioch.virginia.edu/CIRCLE_FINDER_MASTER/hg38.4.bt2 http://genome.bioch.virginia.edu/CIRCLE_FINDER_MASTER/hg38.fa.amb http://genome.bioch.virginia.edu/CIRCLE_FINDER_MASTER/hg38.fa.ann http://genome.bioch.virginia.edu/CIRCLE_FINDER_MASTER/hg38.fa.bwt http://genome.bioch.virginia.edu/CIRCLE_FINDER_MASTER/hg38.fa.fai http://genome.bioch.virginia.edu/CIRCLE_FINDER_MASTER/hg38.fa.pac http://genome.bioch.virginia.edu/CIRCLE_FINDER_MASTER/hg38.fa.sa http://genome.bioch.virginia.edu/CIRCLE_FINDER_MASTER/hg38.rev.1.bt2 http://genome.bioch.virginia.edu/CIRCLE_FINDER_MASTER/hg38.rev.2.bt2

Example download command: wget http://genome.bioch.virginia.edu/CIRCLE_FINDER_MASTER/hg38.fa

Step 5: Download the fastq files. Link to download these files is given in file "fastq-file-download-link.txt"

cat fastq-file-download-link.txt

http://genome.bioch.virginia.edu/CIRCLE_FINDER_MASTER/Index11_1.fq http://genome.bioch.virginia.edu/CIRCLE_FINDER_MASTER/Index11_2.fq

Step 6: You are all set to run the pipeline

bash /path-of-the-"Circle_finder"-directory/microDNA.InOne.sh /path-of-the-"Circle_finder"-directory/hg38 Index11_1.fq Index11_2.fq 24 C4-2 49 10000 /path-of-the-"Circle_finder"-directory &

Step 7: Final output file "microDNA.JT.postmotif.fa"

head microDNA.JT.postmotif.fa chr1 28761 29551 0 1 NOMOTIF

chr1 199385 199915 0 1 GTC

chr1 631932 632604 0 1 NOMOTIF

chr1 632019 632252 1 0 CA

chr1 632112 632242 0 1 T

chr1 889483 890225 4 0 C

chr1 897103 898784 2 0 C

chr1 980217 981339 0 1 G

chr1 982484 982697 1 0 NOMOTIF

chr1 983705 984358 0 2 C

Step 8: Explanation of output

Column 1 "Chromosome name"

Column 2 "start position of circle"

Column 3 "end position of circle"

Column 4 "Number of reads mapping on circle junction from "+" strand"

Column 5 "Number of reads mapping on circle junction from "-" strand"

Column 6 "micro homology (if any) at the junction of circle"

Step 9: If you wish to extract only those circular DNA that has evidence of at least one read mapping on circle junction as "+" and "-" orientation

awk '$4>0 && $5>0' microDNA.JT.postmotif.fa | head

chr1 1069854 1070524 1 2 C

chr1 1069934 1071919 6 2 NOMOTIF

chr1 1070501 1070786 1 2 GAGTC

chr1 1428170 1428595 5 5 NOMOTIF

chr1 1459119 1460224 6 2 NOMOTIF

chr1 1459425 1462380 3 1 GGG

chr1 1495168 1495816 1 3 GG

chr1 1579383 1580962 1 1 GTA

chr1 1667878 1668245 9 6 C

chr1 1772882 1773318 2 3 A