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| Key | Type | Default Value | Description | ||||
|---|---|---|---|---|---|---|---|
| FRAGMENTATION | Boolean | YES | Turn fragmentation on/off. | ||||
| FRAG_SUBSTRATE | {DNA,RNA} | DNA | Substrate of fragmentation, determines the order of fragmentation and reverse transcription (RT): for substrate DNA, fragmentation is carried out after RT, substrate RNA triggers fragmentation before RT. | ||||
| FRAG_METHOD | {EZ,NB,UR} | UR | Fragmentation method employed: * [EZ] Fragmentation by enzymatic digestion * [NB] Fragmentation by nebulization * [UR] Uniformal random fragmentation * [EZ] Fragmentation by enzymatic digestion | ||||
Enzymatic Digestion | |||||||
| FRAG_EZ_MOTIF | String | Sequence motif caused by selective restriction with an enzyme, choose pre-defined NlaIII, DpnII, or a file with a custom position weight matrix. | |||||
| Nebulization | |||||||
| FRAG_NB_LAMBDA | Double | 900.0 | Threshold on molecule length that cannot be broken by the shearfield of nebulization. | ||||
| FRAG_NB_THOLD | Double | 0.1 | Threshold on the fraction of the molecule population; if less molecules break per time unit, convergence to steady state is assumed. | ||||
| FRAG_NB_M | Double | 1.0 | Strength of the nebulization shearfield (i.e., rotor speed). | ||||
| Uniformal Random (UR) Fragmentation | |||||||
| FRAG_UR_ETA | Double | NaN | Average expected framgent size after fragmentations, i.e., number of breaks per unit length (exhautiveness of fragmentation); NaN optimizes the fragmentation process w.r.t. the size filtering | ||||
| FRAG_UR_DELTA | Double | NaN | Geometry of molecules in the UR process: * NaN= depends logarithmically on molecule length, * 1= always linear, * 2= always surface-diameter, * 3= volume-diameter, ... | ||||
| FRAG_UR_D0 | Double | 1.0 | Minimum length of fragments produced by UR fragmentation. | ||||
| Key | Type | Default Value | Description |
| RT_PRIMER | [RANDOM|POLY-DT] | Flag to switch between random priming and poly-dT priming for the first strand synthesis of the reverse transcription | |
| RT_MIN | Integer | Minimum length (in [nt]) of the expected reversely transcribed cDNA molecules | |
| RT_MAX | Integer | Maximum length (in [nt]) of the expected reverse transcription products | |
| FRAGMENTATION | [YES|NO] | Optional: flag that determines whether a fragmentation step is carried out | |
| FRAG_B4_RT | [YES|NO] | flag to schedule the fragmentation before (YES), or after (NO) the reverse transcription. Note for fragmentations carried out before reverse transcription, exclusively random priming strategies are reasonable. | |
| FRAG_MODE | [PHYSICAL|CHEMICAL] | flag to switch between fragmentation according to physical or chemical attributes. | |
| FRAG_LAMBDA | Integer | Upper boundary of fragment lengths (in [nt]) that are not expected to be fragmented by the applied technique | |
| FILTERING | [YES|NO] | Flag to indicate whether a length filtering step is carried out on the cDNA library. | |
| FILT_MIN | Integer | Minimum length that is retained during filtering. | |
| FILT_MAX | Integer | Maximum length that is retained during filtering. | |
| READ_NUMBER | Integer | Number of reads that are intented to produce. Note: this number is an upper boundary and gets adapted to the actual size of the intermediary generated library. | |
| READ_LENGTH | Integer | Length of the generated reads, depends on filtering settings. | |
| PAIRED_END | [YES|NO] | Flag to indicate whether read pairs are produced. | |
| FASTQ | [YES|NO] | Flag that indicates whether additionally the read sequences and qualities are output. Depends on GENOME_DIR and ERR_FNAME. | |
| QTHOLD | Integer | Quality value below which base-calls are considered problematic. | |
| TMP_DIR | String | Path to folder for temporary files, if different from system standard (commonly /tmp on Unix clones). |
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