AccuraCode contains interfaces multi_{assay} to generate pipeline scripts for all assays. Assays can be one of:
- accura
Run multi_{assay} -h for help.
-
AccuraCode 384
conda activate accuracode multi_accura\ --mapfile ./mapfile\ --genomeDir /Database/genome/homo\ --thread 8\ --mod shell
--mapfile Required. Mapfile path.
--genomeDir Required. Genome directory after running accuracode accura mkref.
--thread The recommended setting is 8, and the maximum should not exceed 20.
--mod Create sjm(simple job manager https://github.com/StanfordBioinformatics/SJM) or shell scripts.
--skip_umi_correct For a large data set, users can set it to skip umi corretion to boost speed.
Scripts above will generate a shell directory containing {sample}.sh files.
You can start your analysis by running:
sh ./shell/{sample}.sh
- part of AccuraCode 384
conda activate accuracode multi_accura \ --mapfile ./mapfile \ --genomeDir /Database/genome/homo \ --thread 8 \ --mod shell \ --whitelist /path/to/wellbarcode/file
If you use part of the wells, we recommend you set the "--whitelist" parameter and write the well barcodes you used into a wellbarcode file.
The wellbarcoe file format is one barcode per line, eg:
AACGGACCT
GACTGGTTG
TCGGTTCGT
GTCTTGCGT
or two columns per line (2nd col showed in report and final matrix), eg:
AACGGACCT A01
GACTGGTTG A02
TCGGTTCGT B01
GTCTTGCGT B02
Mapfile is a tab-delimited text file with as least three columns. Each line of mapfile represents paired-end fastq files.
1st column: Fastq file prefix.
2nd column: Fastq file directory path.
3rd column: Sample name, which is the prefix of all output files.
Sample1 has 2 paired-end fastq files located in 2 different directories(fastq_dir1 and fastq_dir2). Sample2 has 1 paired-end fastq file located in fastq_dir1.
$cat ./my.mapfile
fastq_prefix1 fastq_dir1 sample1
fastq_prefix2 fastq_dir2 sample1
fastq_prefix3 fastq_dir1 sample2
$ls fastq_dir1
fastq_prefix1_1.fq.gz fastq_prefix1_2.fq.gz
fastq_prefix3_1.fq.gz fastq_prefix3_2.fq.gz
$ls fastq_dir2
fastq_prefix2_1.fq.gz fastq_prefix2_2.fq.gz