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config-ncrna.txt file to define options according to the descriptions of options below (Table 3) and also inside the file. In the config-ncrna.txt file, you may find more options than that in the web page, especially for the Bowtie mapping step, but we do not suggest you to make any changes in these extra options unless you are an expert.
| gray Options | Description |
|---|---|
| LOGFILE | File that lists actions that have occurred during the analysis |
| N_CPU | Number of CPU used by Bowtie to do mapping |
| FASTQ_FORMAT | The quality score format of the fastq reads. Three formats are supported: phred33 (Sanger, Solexa version 1.8 or later), solexa (Solexa prior to version 1.3), solexa1.3 (Solexa version 1.3 to 1.7) |
| BOWTIE_GENOME_REFERENCE | Basename of the Bowtie index genome reference file (base space). See the http://bowtie-bio.sourceforge.net/manual.shtml Bowtie manual for additional informations |
| BOWTIE_GENOME_REFERENCE_CS | Basename of the Bowtie index genome reference file (color space). See the http://bowtie-bio.sourceforge.net/manual.shtml Bowtie manual for additional informations |
| BOWTIE_GENOME_OPTIONS_FQ | Options for Bowtie to map base space reads in fastq format (Solexa) |
| BOWTIE_GENOME_OPTIONS_FA | Options for Bowtie to map base space reads in fasta format (454) |
| BOWTIE_GENOME_OPTIONS_CS | Options for Bowtie to map color space reads (SOLiD) |
| GROUP_READ | Group reads based on their sequence for raw reads before mapping or read alignments in bam file depending on the input format. 1: Yes; 0: No; 2: for the online version where the input files have already been grouped using our provided scripts |
| ORGANISM | Name of the reference organism. Must be the same as the organism available in the annotation folder (i.e. mm9, hg19, ...) |
| MATURE_MIRNA | Annotation against miRNAs from miRBase. Both miRNA with and without an extended item are acceptable (see 5.4.2) |
| PRECURSOR_MIRNA | Annotation against pre-miRNAs from miRBase. Both miRNA with and without an extended item are acceptable (see 5.4.2) |
| NCRNA_RFAM | List of the RFAM ncRNA(s) to focus on (comma separator) - no extension parameter |
| NCRNA_RFAM_EX | List of the RFAM ncRNA(s) to focus on (comma separator) - extension parameter (see 5.4.2) |
| NCRNA_RMSK | List of the repetitive elements to focus on (comma separator) - no extension parameter |
| NCRNA_RMSK_EX | List of the repetitive elements to focus on (comma separator) - extension parameter (see 5.4.2) |
| TRNA_UCSC | Mapping against tRNA sequences. Both tRNA with and without an extended item are acceptable (see 5.4.2) |
| OTHER_NCRNA_GFF | List of custom gff files to intersect with the mapped reads |
| LOGO_DIRECTION | Align the sequence on the 5' or 3' end [5/3] |
| IC_SCALE | Use the information content scale for Logo outputs. 1: Yes; 0: No |
| GENOME_TRACK_OPTIONS | Options to select reads mapped in the genome to generate track file. Four options should be provided to filter reads, and separated by comma. min_len=N : the minimum length (N) of read; max_len=N: the maximum length (N) of read; min_copy=N : the minimum number (N) of matches in the genome; max_copy=N: the maximum number (N) of matches in the genome. To have more than one type of track, different sets of options should be separated by pipe ( ) |
| SIG_READ_OPTIONS | Options to select mapped reads for enrichment analysis (see 5.5). Please refer to the format of GENOME_TRACK_OPTIONS |
| SIG_WIN_SIZE | The window size used to scan the genome (e.g. 10000) (see 5.5) |
| SIG_STEP_SIZE | The step size (e.g. 50000) (see 5.5) |
| EXCLUDE_ANN_GFF | List of annotation files (gff3). Only reads which are not mapped in these annotated regions are kept for enrichment analysis (see 5.5) |
| FIT_MODEL | The model used to fit window-based read distribution. Three models can be chosen: NB.ML, NB.012, and Poisson (see 5.5) |
| PVAL_CUTOFF | The cut-off used to get regions significantly enriched with reads |
Nicolas Servant 2012-05-31