Parameters¶
The following table lists the currently available parameters for CIPHER along with a brief description. Updated: May 2017
REQUIRED PARAMETERS
| Parameter | Description |
|---|---|
| –mode | Choose from available: ‘chip’, ‘rna’, ‘gro’, ‘mnase’, ‘dnase’ , ‘atac’, ‘analysis’. |
| –config | Tab separated config file with sample information. Check README for more information. |
| –fasta | Reference genome in FASTA format. |
| –gtf | Reference genome in GTF format. |
| –lib | Library information. “s” for single-stranded data, “p” for pair-ended data. |
| –readLen | The length of your reads. |
RNA-seq MODE ONLY
| Parameter | Description | |||
|---|---|---|---|---|
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ANALYSIS MODE ONLY
| Parameter | Description | |||
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OPTIONAL PARAMETERS
| Parameter | Description | Default Value |
|---|---|---|
| –threads | Number of threads to use. | 1 |
| –aligner | The alignment software for mapping reads. Available: bbmap, star, hisat2, bwa, bowtie2. | bbmap |
| –minid | Minimum alignment identity to look for during BBMap mapping. Higher is faster and less sensitive. | 0.76 |
| –qvalue | Minimum FDR cutoff for peak detection in MACS2 ad EPIC. | 0.01 |
| –epic_w | Window size ued to scan the genome for peak detection in EPIC. | 200 |
| –epic_g | A multiple of epic_w used to determine the gap size in EPIC. | 3 |
| –maxindel | Maximum indel length searched during mapping. 200k recommended for vertebrate genomes. | 200k |
| –intronlen | Maximum intron length during mapping. 20 recommended for vertebrate genomes. | 20 |
| –egs | The effective genome size of your species. Is automatically calculated by default. 80GB of RAM. | Auto |
| –egs_ratio | Effective genome as fraction of genome size. Must be between 0 and 1. Automatically calculated. | Auto |
| –outdir | Name of ourput directory. | results |
ALIGNER-SPECIFIC OPTIONAL PARAMETERS
BWA
| Parameter | Description | Default Value |
|---|---|---|
| –bwa_k | See -k option in BWA user manual for more information. | 19 |
| –bwa_w | See -w option in BWA user manual for more information. | 100 |
| –bwa_d | See -d option in BWA user manual for more information. | 19 |
| –bwa_r | See -r option in BWA user manual for more information. | 1.5 |
| –bwa_c | See -c option in BWA user manual for more information. | 10000 |
| –bwa_A | See -A option in BWA user manual for more information. | 1 |
| –bwa_B | See -B option in BWA user manual for more information. | 4 |
| –bwa_O | See -O option in BWA user manual for more information. | 6 |
| –bwa_E | See -E option in BWA user manual for more information. | 1 |
| –bwa_L | See -L option in BWA user manual for more information. | 5 |
| –bwa_U | See -U option in BWA user manual for more information. | 9 |
| –bwa_T | See -T option in BWA user manual for more information. | 30 |
BOWTIE2
| Parameter | Description | Default Value |
|---|---|---|
| –bt2_D | See -D option in Bowtie2 user manual for more information. | 20 |
| –bt2_R | See -R option in Bowtie2 user manual for more information. | 3 |
| –bt2_N | See -N option in Bowtie2 user manual for more information. | 0 |
| –bt2_L | See -L option in Bowtie2 user manual for more information. | 20 |
| –bt2_i | See -i option in Bowtie2 user manual for more information. | S,5,1,0.50 |
| –bt2_trim5 | See –trim5 option in Bowtie2 user manual for more information. | 0 |
| –bt2_trim3 | See –trim3 option in Bowtie2 user manual for more information. | 0 |
| –local | Set this parameter to map alignments in local mode. | false |
HISAT2
| Parameter | Description | Default Value |
|---|---|---|
| –hs_k | See -k option in HISAT2 user manual for more information. | 5 |
| –hs_trim5 | See –trim5 option in HISAT2 user manual for more information. | 0 |
| –hs_trim3 | See –trim3 option in HISAT2 user manual for more information. | 0 |
| –hs_mp | See –mp option in HISAT2 user manual for more information. | 6,2 |
| –hs_sp | See –sp option in HISAT2 user manual for more information. | 2,1 |
| –hs_np | See –np option in HISAT2 user manual for more information. | 1 |
| –hs_rdg | See –rdg option in HISAT2 user manual for more information. | 5,3 |
| –hs_rfg | See –rfg option in HISAT2 user manual for more information. | 5,3 |
| –hs_pen_cansplice | See –pen-cansplice option in HISAT2 user manual for more information. | 0 |
| –hs_pen_noncansplice | See –pen-noncansplice option in HISAT2 user manual for more information. | 12 |
| –hs_min_intronlen | See –min-intronlen option in HISAT2 user manual for more information. | 20 |
| –hs_max_intronlen | See –max-intronlen option in HISAT2 user manual for more information. | 500000 |
| –hs_max_seeds | See –max-seeds option in HISAT2 user manual for more information. | 5 |
STAR
| Parameter | Description | Default Value |
|---|---|---|
| –star_clip3pNbases | See –clip3pNbases option in STAR user manual for more information. | 0 |
| –star_clip5pNbases | See –clip5pNbases option in STAR user manual for more information. | 0 |
| –star_outFilterMultimapScoreRange | See –outFilterMultimapScoreRange option in STAR user manual for more information. | 1 |
| –star_outFilterMultimapNmax | See –outFilterMultimapNmax option in STAR user manual for more information. | 10 |
| –star_outFilterMismatchNmax | See –outFilterMismatchNmax option in STAR user manual for more information. | 10 |
| –star_outFilterScoreMin | See –outFilterScoreMin option in STAR user manual for more information. | 0 |
| –star_alignEndsType | See –alignEndsType option in STAR user manual for more information. | Local |
| –star_winAnchorMultimapNmax | See –winAnchorMultimapNmax option in STAR user manual for more information. | 50 |
| –star_quantMode | See –quantMode option in STAR user manual for more information. | |
| –star_twopassMode | See –twopassMode option in STAR user manual for more information. | None |
FOR OPTIMIZING AND TESTING
| Parameter | Description | Default Value |
|---|---|---|
| –subsample | Set this flag to subsample reads for teting. | false |