Short read mapping
usage: ecc_finder.py map-sr <reference.idx> <query.fq>
A tool to detect eccDNA loci using Illumina read sequencing
positional arguments:
<reference.idx> index file of reference genome
<query.fq1> query fastq forward file (uncompressed or bgzipped)
<query.fq2> query fastq reverse file (uncompressed or bgzipped)
optional arguments:
-h, --help show this help message and exit
map options:
-t INT number of CPU threads for mapping mode
--aligner PATH short read aligner executable ('bwa', 'bowtie2','segemehl','minimap2') [bwa]
--bwa-params STR space delimted bwa parameters [' mem ']
--bowtie2-params STR space delimted bowtie2 parameters ['--end-to-end -k 1 --sensitive']
--segemehl-params STR
space delimted segemehl parameters ['-S -A 95 -W 95 -U 24 -Z 25 -t 8']
--minimap2-params STR
space delimted minimap2 parameters [' -ax sr ']
-g STR reference genome size larger than 4Gb [yes]
peak-calling options:
-l INT minimum length of a peak [200]
-d INT maximum distance between signif. sites [1000]
-p FLT maximum p-value [0.05]
validation options:
-r <reference.fa> reference genome fasta (uncompressed or bgzipped)
--min-read INT filter locus by unique mapped read number [3]
--min-cov FLT filter locus at regions by raw read coverage (# aligned bases / total bases)
output options:
-o PATH output directory [./eccFinder_output]
-w overwrite intermediate files
-x X add prefix to output [ecc.ill]
All output is in eccFinder_output, or whichever directory -o specifies.
ecc.sr.fasta
The eccDNA locus in FASTA format.
ecc.sr.csv
The eccDNA locus in csv format.
| Col | Type | Description |
|---|---|---|
| 1 | string | Reference sequence name |
| 2 | int | Reference start on original strand |
| 3 | int | Reference end on original strand |
| 4 | int | Circular read number at the locus |
| 5 | int | Repeat units of all circular reads |
| 6 | int | Read coverage at the locus |
| 7 | int | EccDNA sequence length |
ecc_finder.png
The Size distribution of detected eccDNA in png format.
