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comparison multigps.xml @ 41:844033a58b65 draft

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author greg
date Wed, 14 Dec 2016 11:31:49 -0500
parents 55202c4e2da6
children 8d30aeacb52a
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40:55202c4e2da6 41:844033a58b65
443 ----- 443 -----
444 444
445 **Options** 445 **Options**
446 446
447 * **Loading data:** 447 * **Loading data:**
448
448 - **Optional file containing file containing reads from a control experiment** - must be same format as input experiment 449 - **Optional file containing file containing reads from a control experiment** - must be same format as input experiment
449 - **Fixed per-base limit** - Fixed per-base limit (default: estimated from background model). 450 - **Fixed per-base limit** - Fixed per-base limit (default: estimated from background model).
450 - **Poisson threshold for filtering per base** - Look at neighboring positions to decide what the per-base limit should be. 451 - **Poisson threshold for filtering per base** - Look at neighboring positions to decide what the per-base limit should be.
451 - **Use non-unique reads** - Use non-unique reads. 452 - **Use non-unique reads** - Use non-unique reads.
452 - **Fraction of the genome that is mappable for these experiments** - Fraction of the genome that is mappable for these experiments 453 - **Fraction of the genome that is mappable for these experiments** - Fraction of the genome that is mappable for these experiments
453 - **Turn off caching of the entire set of experiments?** - Flag to turn off caching of the entire set of experiments (i.e. run slower with less memory). 454 - **Turn off caching of the entire set of experiments?** - Flag to turn off caching of the entire set of experiments (i.e. run slower with less memory).
454 455
455 * **Scaling control vs signal counts:** 456 * **Scaling control vs signal counts:**
457
456 - **Use signal vs control scaling?** - Flag to turn off auto estimation of signal vs control scaling factor 458 - **Use signal vs control scaling?** - Flag to turn off auto estimation of signal vs control scaling factor
457 - **Use the median signal/control ratio as the scaling factor?** - Flag to use scaling by median ratio (default = scaling by NCIS). 459 - **Use the median signal/control ratio as the scaling factor?** - Flag to use scaling by median ratio (default = scaling by NCIS).
458 - **Use scaling by regression on binned tag counts?** - Flag to use scaling by regression (default = scaling by NCIS). 460 - **Use scaling by regression on binned tag counts?** - Flag to use scaling by regression (default = scaling by NCIS).
459 - **Estimate scaling factor by SES?** - Specify whether to estimate scaling factor by SES. 461 - **Estimate scaling factor by SES?** - Specify whether to estimate scaling factor by SES.
460 - **Multiply control counts by total tag count ratio and then by this factor** - Multiply control counts by total tag count ratio and then by this factor (default: NCIS). 462 - **Multiply control counts by total tag count ratio and then by this factor** - Multiply control counts by total tag count ratio and then by this factor (default: NCIS).
461 - **Window size for estimating scaling ratios** - Window size in base pairs for estimating scaling ratios 463 - **Window size for estimating scaling ratios** - Window size in base pairs for estimating scaling ratios
462 - **Plot diagnostic information for the chosen scaling method?** - Flag to plot diagnostic information for the chosen scaling method. 464 - **Plot diagnostic information for the chosen scaling method?** - Flag to plot diagnostic information for the chosen scaling method.
463 465
464 * **Running MultiGPS:** 466 * **Running MultiGPS:**
467
465 - **binding event read distribution file** - Binding event read distribution file for initializing models. The true distribution of reads around binding events is estimated during MultiGPS training. A default initial distribution appropriate for ChIP-seq data is used if this option is not specified. 468 - **binding event read distribution file** - Binding event read distribution file for initializing models. The true distribution of reads around binding events is estimated during MultiGPS training. A default initial distribution appropriate for ChIP-seq data is used if this option is not specified.
466 - **Maximum number of training rounds for updating binding event read distributions** - Maximum number of training rounds for updating binding event read distributions. 469 - **Maximum number of training rounds for updating binding event read distributions** - Maximum number of training rounds for updating binding event read distributions.
467 - **Perform binding model updates?** - Perform binding model updates? 470 - **Perform binding model updates?** - Perform binding model updates?
468 - **Minimum number of events to support an update of the read distribution** - Minimum number of events to support an update of the read distribution 471 - **Minimum number of events to support an update of the read distribution** - Minimum number of events to support an update of the read distribution
469 - **Perform binding model smoothing?** - Smooth with a cubic spline using a specified smoothing factor. 472 - **Perform binding model smoothing?** - Smooth with a cubic spline using a specified smoothing factor.
476 - **Impose this alpha** - The alpha parameter is a sparse prior on binding events in the MultiGPS model. It can be interpreted as a minimum number of reads that each binding event must be responsible for in the model. Default: estimate alpha automatically. 479 - **Impose this alpha** - The alpha parameter is a sparse prior on binding events in the MultiGPS model. It can be interpreted as a minimum number of reads that each binding event must be responsible for in the model. Default: estimate alpha automatically.
477 - **Share component configs in the ML step?** - Flag to not share component configs in the ML step 480 - **Share component configs in the ML step?** - Flag to not share component configs in the ML step
478 - **Optional file containing a set of regions to ignore during MultiGPS training** - File containing a set of regions to ignore during MultiGPS training. It’s a good idea to exclude the mitochondrial genome and other ‘blacklisted’ regions that contain artifactual accumulations of reads in both ChIP-seq and control experiments. MultiGPS will waste time trying to model binding events in these regions, even though they will not typically appear significantly enriched over the control (and thus will not be reported to the user). 481 - **Optional file containing a set of regions to ignore during MultiGPS training** - File containing a set of regions to ignore during MultiGPS training. It’s a good idea to exclude the mitochondrial genome and other ‘blacklisted’ regions that contain artifactual accumulations of reads in both ChIP-seq and control experiments. MultiGPS will waste time trying to model binding events in these regions, even though they will not typically appear significantly enriched over the control (and thus will not be reported to the user).
479 482
480 * **MultiGPS priors:** 483 * **MultiGPS priors:**
484
481 - **Perform inter-experiment positional prior?** - Flag to turn off inter-experiment positional prior (default=on). 485 - **Perform inter-experiment positional prior?** - Flag to turn off inter-experiment positional prior (default=on).
482 - **Probability that events are shared across conditions** - Probability that events are shared across conditions. 486 - **Probability that events are shared across conditions** - Probability that events are shared across conditions.
483 - **Perform both motif-finding and motif priors?** - Flag to turn off motif-finding and motif priors. 487 - **Perform both motif-finding and motif priors?** - Flag to turn off motif-finding and motif priors.
484 - **Perform motif-finding only?** - Flag to turn off motif priors only. 488 - **Perform motif-finding only?** - Flag to turn off motif priors only.
485 - **Number of motifs MEME should find for each condition** - Number of motifs MEME should find for each condition. 489 - **Number of motifs MEME should find for each condition** - Number of motifs MEME should find for each condition.
486 - **Minimum motif width for MEME** - minw arg for MEME. 490 - **Minimum motif width for MEME** - minw arg for MEME.
487 - **Maximum motif width for MEME** - maxw arg for MEME. 491 - **Maximum motif width for MEME** - maxw arg for MEME.
488 492
489 * **Reporting binding events:** 493 * **Reporting binding events:**
494
490 - **Minimum Q-value (corrected p-value) of reported binding events** - Minimum Q-value (corrected p-value) of reported binding events. 495 - **Minimum Q-value (corrected p-value) of reported binding events** - Minimum Q-value (corrected p-value) of reported binding events.
491 - **Minimum event fold-change vs scaled control** - Minimum event fold-change vs scaled control. 496 - **Minimum event fold-change vs scaled control** - Minimum event fold-change vs scaled control.
492 - **Run differential enrichment tests?** - Choose whether to run differential enrichment tests. 497 - **Run differential enrichment tests?** - Choose whether to run differential enrichment tests.
493 - **EdgeR over-dispersion parameter value** - EdgeR over-dispersion parameter value. 498 - **EdgeR over-dispersion parameter value** - EdgeR over-dispersion parameter value.
494 - **Minimum p-value for reporting differential enrichment** - Minimum p-value for reporting differential enrichment. 499 - **Minimum p-value for reporting differential enrichment** - Minimum p-value for reporting differential enrichment.
500
495 </help> 501 </help>
496 <expand macro="citations" /> 502 <expand macro="citations" />
497 </tool> 503 </tool>