Command line arguments
We provide 3 scripts to run the analysis and visualize nanopore data as the following.
alignment_magnifier
| Argument name | Required | Description |
|---|---|---|
| -i, --input_fastq | Yes | input FASTQ file |
| -c, --control_fastq | No | control FASTQ file, will run as single-mode if missing |
| -o, --output | No | output folder's name (Default:nanoCEM_result) |
| --chrom | Yes | gene/transcript or chromosome name (header of your reference file) |
| --pos | Yes | Site of your interest (1-based) |
| -r, --ref | Yes | reference file (fasta/fna/fa) |
| --len | No | region around the position (Default:10) |
| -t,--cpu | No | number of processes (Default:4) |
| --strand | No | strand of your interest (Default:+) |
| --rna | No | turn on the RNA mode (Default:False) |
| -h, --help | No | show this help message and exit |
current_events_magnifier
These are some differences in parameters when using "current_events_magnifier" with f5c_re, f5c_ev, tombo and move_table tools.
For f5c_re and f5c_ev, the argument is same,
current_events_magnifier f5c_re -h
current_events_magnifier f5c_ev -h
| Argument name | Required | Description |
|---|---|---|
| -i, --input | Yes | the input files' prefix |
| -c, --control | No | the control files' prefix, will run as single-mode if missing |
| -o, --output | No | output_file (Default:nanoCEM_result) |
| --ref | Yes | reference file (fasta/fna/fa) |
| --chrom | Yes | gene/transcript or chromosome name (header of your reference file) |
| --pos | Yes | site of your interest (1-based) |
| --len | No | region around the position (Default:10) |
| -t, --cpu | No | num of process (Default:8) |
| -s, --subsample-ratio | No | ratio of reads will be used to plot (Default:1) |
| --strand | No | strand of your interest (Default:+) |
| --rna | No | turn on the RNA mode (Default:False) |
| --norm | No | turn on the normalization (Default:False) |
| --base_shift | No | to shift the ref,choose from auto,0,-1,-2,-3,-4,-5,-6,-7,-8 (Default:auto) |
| --pore | No | type of pore choose from r9, r10, rna004 (Default: r9) |
| --kmer_size | No | kmer size for the PCA and MANOVA analysis (Default:3) |
| -h, --help | No | Show this help message and exit |
For tombo, you can view it for
current_events_magnifier tombo -h
| Argument name | Required | Description |
|---|---|---|
| -i, --fast5 | Yes | the input single-format fast5's folder |
| -c, --control_fast5 | No | the control single-format fast5's folder, will run as single-mode if missing |
| -o, --output | No | output_file (Default:nanoCEM_result) |
| --ref | Yes | reference file (fasta/fna/fa) |
| --chrom | Yes | gene/transcript or chromosome name (header of your fasta file) |
| --pos | Yes | site of your interest (1-based) |
| --len | No | region around the position (Default:10) |
| -t, --cpu | No | num of process (Default:8) |
| -s,--subsample-ratio | No | ratio of reads will be used to plot (Default:1) |
| --strand | No | strand of your interest (Default:+) |
| --rna | No | turn on the RNA mode (Default:False) |
| --norm | No | turn on the normalization (Default:False) |
| --basecall_group | No | re-squiggle result index information into.(Default:RawGenomeCorrected_000) |
| --basecall_subgroup | No | basecall sequence inforamtion into. (Default:BaseCalled_template) |
| --kmer_size | No | kmer size for the PCA and MANOVA analysis (Default:3) |
| -h, --help | No | Show this help message and exit |
And move_table,
current_events_magnifier move_table -h
| Argument name | Required | Description |
|---|---|---|
| -i, --input | Yes | the input files' prefix |
| -c, --control | No | the control files' prefix, will run as single-mode if missing |
| -o, --output | No | output_file (Default:nanoCEM_result) |
| --ref | Yes | reference file (fasta/fna/fa) |
| --chrom | Yes | gene/transcript or chromosome name (header of your reference file) |
| -m, --sig_move_offset | Yes | sig_move_offset for squigualiser reform |
| -k, --kmer_length | Yes | kmer_length for squigualiser reform |
| --pos | Yes | site of your interest (1-based) |
| --len | No | region around the position (Default:10) |
| -t, --cpu | No | num of process (Default:8) |
| -s, --subsample-ratio | No | ratio of reads will be used to plot (Default:1) |
| --strand | No | strand of your interest (Default:+) |
| --rna | No | turn on the RNA mode (Default:False) |
| --norm | No | turn on the normalization (Default:False) |
| --kmer_size | No | kmer size for the PCA and MANOVA analysis (Default:3) |
| -h, --help | No | Show this help message and exit |
extract_sub_fast5_from_bam
To extract a subset of a single-format fast5 and saved in new folder. If you do not input an interest region, all the reads that have been aligned will be saved in the new folder.
| Argument name | Required | Description |
|---|---|---|
| -f, --fast5 | Yes | path to single-format fast5 files |
| -b, --bam | Yes | path to bam file |
| -o, --output | No | output file (Default:subsample_single) |
| -t, --cpu | No | number of processes (Default:4) |
| --chrom | No | gene/transcript or chromosome name (header of your reference file) |
| --pos | No | site of your interest (1-based) |
| -h, --help | No | show this help message and exit |