Difference between revisions of "Ribo-Seq and mRNA features forming (analysis)"
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==== Parameters: ==== | ==== Parameters: ==== | ||
| − | * ''' | + | * '''Data set name''' – Select data set |
| − | + | ||
* '''Sequences collection''' – Select a source of nucleotide sequences | * '''Sequences collection''' – Select a source of nucleotide sequences | ||
** '''Sequences source''' – Select database to get sequences from or <nowiki>'</nowiki>Custom<nowiki>'</nowiki> to specify sequences location manually | ** '''Sequences source''' – Select database to get sequences from or <nowiki>'</nowiki>Custom<nowiki>'</nowiki> to specify sequences location manually | ||
** '''Sequence collection''' – Specify path to folder containing sequences if <nowiki>'</nowiki>Custom<nowiki>'</nowiki> sequences source is selected | ** '''Sequence collection''' – Specify path to folder containing sequences if <nowiki>'</nowiki>Custom<nowiki>'</nowiki> sequences source is selected | ||
| − | * ''' | + | * '''Two tables for calculation of translation (initiation) efficiency, TE (TIE)''' – Two tables for calculation of translation (initiation) efficiency, TE (TIE) |
| − | * ''' | + | ** '''Path to table with mRNA-Seq data''' – Path to table with mRNA-Seq data |
| + | ** '''Column name with mRNA-Seq reads number''' – Select column name with mRNA-Seq reads number | ||
| + | ** '''mRNA-Seq reads threshold''' – Transcripts for which mRNA-Seq reads number are grater than this threshold will be considered only | ||
| + | ** '''Path to table with Ribo-Seq data''' – Path to table with Ribo-Seq data | ||
| + | ** '''Column name with Ribo-Seq reads number''' – Select column name with Ribo-Seq reads number | ||
| + | ** '''Ribo-Seq reads threshold''' – Transcripts for which Ribo-Seq reads number are grater than this threshold will be considered only | ||
| + | ** '''Column name with start codon positions''' – Select column name with start codon positions | ||
| + | ** '''Column name with transcript names''' – Column name with transcript names | ||
| + | * '''Path to folder with special data sets''' – Path to folder with special data sets | ||
* '''Start codon type''' – Start codon type | * '''Start codon type''' – Start codon type | ||
| + | * '''Order of start codon''' – Order of start codon | ||
* '''mRNA and Ribo-Seq features''' – Select mRNA and Ribo-Seq features | * '''mRNA and Ribo-Seq features''' – Select mRNA and Ribo-Seq features | ||
| + | * '''Sequence sample''' – Sequence sample | ||
| + | ** '''Are mRNA fragments near start codons?''' – Are mRNA fragments near start codons (or near stop codons)? | ||
| + | ** '''Left boundary of each mRNA fragment''' – Left boundary of each mRNA fragment with respect to start (or stop) codon | ||
| + | ** '''Right boundary of each mRNA fragment''' – Right boundary of each mRNA fragment with respect to start (or stop) codon | ||
| + | * '''Paths to matrices''' – Paths to matrices | ||
* '''Do exclude missing data?''' – Do exclude missing data? (If <nowiki>'</nowiki>no<nowiki>'</nowiki> then possible missing data will be included as NaN-values | * '''Do exclude missing data?''' – Do exclude missing data? (If <nowiki>'</nowiki>no<nowiki>'</nowiki> then possible missing data will be included as NaN-values | ||
* '''Output table path''' – Path to the output table | * '''Output table path''' – Path to the output table | ||
Latest revision as of 19:00, 13 February 2017
- Analysis title
Ribo-Seq and mRNA features forming
- Provider
- Institute of Systems Biology
- Class
RiboSeqAndMrnaFeaturesForming- Plugin
- biouml.plugins.bindingregions (Binding-regions related analyses)
[edit] Description
Create data matrix with Ribo-Seq and mRNA features and write it as TableDataCollection
[edit] Parameters:
- Data set name – Select data set
- Sequences collection – Select a source of nucleotide sequences
- Sequences source – Select database to get sequences from or 'Custom' to specify sequences location manually
- Sequence collection – Specify path to folder containing sequences if 'Custom' sequences source is selected
- Two tables for calculation of translation (initiation) efficiency, TE (TIE) – Two tables for calculation of translation (initiation) efficiency, TE (TIE)
- Path to table with mRNA-Seq data – Path to table with mRNA-Seq data
- Column name with mRNA-Seq reads number – Select column name with mRNA-Seq reads number
- mRNA-Seq reads threshold – Transcripts for which mRNA-Seq reads number are grater than this threshold will be considered only
- Path to table with Ribo-Seq data – Path to table with Ribo-Seq data
- Column name with Ribo-Seq reads number – Select column name with Ribo-Seq reads number
- Ribo-Seq reads threshold – Transcripts for which Ribo-Seq reads number are grater than this threshold will be considered only
- Column name with start codon positions – Select column name with start codon positions
- Column name with transcript names – Column name with transcript names
- Path to folder with special data sets – Path to folder with special data sets
- Start codon type – Start codon type
- Order of start codon – Order of start codon
- mRNA and Ribo-Seq features – Select mRNA and Ribo-Seq features
- Sequence sample – Sequence sample
- Are mRNA fragments near start codons? – Are mRNA fragments near start codons (or near stop codons)?
- Left boundary of each mRNA fragment – Left boundary of each mRNA fragment with respect to start (or stop) codon
- Right boundary of each mRNA fragment – Right boundary of each mRNA fragment with respect to start (or stop) codon
- Paths to matrices – Paths to matrices
- Do exclude missing data? – Do exclude missing data? (If 'no' then possible missing data will be included as NaN-values
- Output table path – Path to the output table
