Commit 7b59581d authored by Sander Bollen's avatar Sander Bollen
Browse files

update readme

parent bfcd47f5
......@@ -6,7 +6,7 @@ Prinia is a python package for designing primers from genomic regions or LOVD im
Requirements
-------------
You must have a recent version of [primer3](http://primer3.sourceforge.net/) and [blat](http://sourceforge.net/projects/blat/files/Blat%20Full%20Version/)
You must have a recent version of [primer3](http://primer3.sourceforge.net/), [samtools](http://www.htslib.org/download/) and [bwa](https://github.com/lh3/bwa)
Furthermore, the following python packages are required:
......@@ -48,12 +48,13 @@ This tool will generate your primers from BED records (regions) or LOVD import f
```
usage: primerdesign [-h] (-l LOVD | --region REGION) [-p PADDING]
(-x XML | -t TSV) [-s SAMPLE]
[--product_size PRODUCT_SIZE]
[--n_raw_primers N_RAW_PRIMERS] [--m13]
(-x XML | -t TSV) -b BAM [-s SAMPLE]
[--product_size PRODUCT_SIZE] [--min-margin MIN_MARGIN]
[--strict] [--n_raw_primers N_RAW_PRIMERS] [--m13]
[--m13-forward M13_FORWARD] [--m13-reverse M13_REVERSE]
[-f FIELD] [-af ALLELE_FREQ] -R REFERENCE --dbsnp DBSNP
--primer3 PRIMER3 --blat BLAT
[-f FIELD] [-af ALLELE_FREQ] [-fq1 FQ1] [-fq2 FQ2] -R
REFERENCE --dbsnp DBSNP --primer3 PRIMER3 [--bwa BWA]
[--samtools SAMTOOLS] [--ignore-errors]
optional arguments:
-h, --help show this help message and exit
......@@ -64,12 +65,17 @@ optional arguments:
to 100
-x XML, --xml XML Output Miracle XML file
-t TSV, --tsv TSV Output TSV file
-b BAM, --bam BAM Path to output BAM file containing primers
-s SAMPLE, --sample SAMPLE
Same ID for regions
--product_size PRODUCT_SIZE
Size range of desired product. Defaults to 200-450
This will be taken as a minimum product size in the
case of regions
--min-margin MIN_MARGIN
Minimum distance from region or variant. Default = 10
--strict Enable strict mode. Primers with products larger than
max product size will NOT be returned
--n_raw_primers N_RAW_PRIMERS
Amount of raw primers from primer3 output that will be
considered. By default, only the top 4 primers (in
......@@ -85,11 +91,19 @@ optional arguments:
Name of field in DBSNP file for allele frequency
-af ALLELE_FREQ, --allele-freq ALLELE_FREQ
Max accepted allele freq
-fq1 FQ1 Path to forward fastq file for primer output. Set if
you want to export your primers in fastq format
(qualities will be sanger-encoded 40)
-fq2 FQ2 Path to reverse fastq file for primer output. Set if
you want to export your primers in fastq format
(qualities will be sanger-encoded 40)
-R REFERENCE, --reference REFERENCE
Path to reference fasta file
--dbsnp DBSNP Path to DBSNP vcf
--primer3 PRIMER3 Path to primer3 exe
--blat BLAT Path to blat exe
--primer3 PRIMER3 Path to primer3_core exe
--bwa BWA Path to BWA exe
--samtools SAMTOOLS Path to samtools exe
--ignore-errors Ignore errors
```
......@@ -111,8 +125,12 @@ The following arguments are mandatory:
* `-R`: path to reference fasta. This fasta *must* have a `.fai` index. Generate this with `samtools faidx <fasta>`
* `--dbsnp`: Path to DBSNP VCF file
* `--primer3`: Path to primer 3 executable. On the SHARK cluster, this is `/usr/bin/primer3_core`
* `--blat`: Path to blat executable. On the SHARK cluster, this is `/usr/local/bin/blat`
* `--primer3`: Path to primer 3 executable.
Recommended arguments:
* `--samtools`: Path to samtools. If not given, will simply assume `samtools` is on the PATH.
* `--bwa`: Path to bwa. If not given, will simply assume `bwa` is on the PATH.
Known issues
......
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