Performs peak calling for ChIP-Seq dataCufflinks accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols.
Parameters in GUI
| Parameter | Description | Default value |
|---|---|---|
| Output directory | Directory to save MACS output files. | |
| Name | The name string of the experiment. MACS will use this string NAME to create output files like 'NAME_peaks.xls', 'NAME_negative_peaks.xls', 'NAME_peaks.bed', 'NAME_summits.bed', 'NAME_model.r' and so on. So please avoid any confliction between these filenames and your existing files (--name). | |
| Wiggle output | If this flag is on, MACS will store the fragment pileup in wiggle format for the whole genome data instead of for every chromosomes (--wig) (--single-profile). | hg19 |
| Wiggle space | By default, the resolution for saving wiggle files is 10 bps,i.e., MACS will save the raw tag count every 10 bps. You can change it along with '--wig' option (--space). | 3000 |
| Genome size (Mbp) | Homo sapience - 2700 Mbp Mus musculus - 1870 Mbp Caenorhabditis elegans - 90 Mbp Drosophila melanogaster - 120 Mbp It's the mappable genome size or effective genome size which is defined as the genome size which can be sequenced. Because of the repetitive features on the chromosomes, the actual mappable genome size will be smaller than the original size, about 90% or 70% of the genome size (--gsize). | 50 |
| P-value | P-value cutoff. Default is 0.00001, for looser results, try 0.001 instead (--pvalue). | 3000 |
| Tag size (optional) | Length of reads. Determined from first 10 reads if not specified (input 0) (--tsize). | 5000 |
| Keep duplicates | It controls the MACS behavior towards duplicate tags at the exact same location -- the same coordination and the same strand. The default auto option makes MACS calculate the maximum tags at the exact same location based on binomal distribution using 1e-5 as pvalue cutoff; and the all option keeps every tags. If an integer is given, at most this number of tags will be kept at the same location (--keep-dup). | 3000 |
| Use model | Whether or not to use MACS paired peaks model (--nomodel). | |
| Model fold | Select the regions within MFOLD range of high-confidence enrichment ratio against. Model fold is available when Use model is true, which is the foldchange to chose paired peaks to build paired peaks model. Users need to set a lower(smaller) and upper(larger) number for fold change so that MACS will only use the peaks within these foldchange range to build model (--mfold). | |
| Shift size | An arbitrary shift value used as a half of the fragment size when model is not built. Shift size is available when Use model is false, which will represent the HALF of the fragment size of your sample. If your sonication and size selection size is 300 bps, after you trim out nearly 100 bps adapters, the fragment size is about 200 bps, so you can specify 100 here (--shiftsize). | |
| Band width | The band width which is used to scan the genome for model building. You can set this parameter as the sonication fragment size expected from wet experiment. Used only while building the shifting model (--bw). | |
| Use lambda | Whether to use local lambda model which can use the local bias at peak regions to throw out false positives (--nolambda). | |
| Small nearby region | The small nearby region in basepairs to calculate dynamic lambda. This is used to capture the bias near the peak summit region. Invalid if there is no control data (--slocal). | |
| Large nearby region | The large nearby region in basepairs to calculate dynamic lambda. This is used to capture the surround bias (--llocal). | |
| Auto bimodal | Whether turn on the auto pair model process.If set, when MACS failed to build paired model, it will use the nomodelsettings, the Shift size parameter to shift and extend each tags (--on-auto). | |
| Scale to large | When set, scale the small sample up to the bigger sample.By default, the bigger dataset will be scaled down towards the smaller dataset,which will lead to smaller p/qvalues and more specific results.Keep in mind that scaling down will bring down background noise more (--to-large). |
Parameters in Schema File
Type: macs-id| Reference annotation | Tells Cufflinks to use the supplied reference annotation to estimate isoform expression. Cufflinks will not assemble novel transcripts and the program will ignore alignments not structurally compatible with any reference transcript. | |
| RABT annotation | Tells Cufflinks to use the supplied reference annotation to guide Reference Annotation Based Transcript (RABT) assembly. Reference transcripts will be tiled with faux-reads to provide additional information in assembly. Output will include all reference transcripts as well as any novel genes and isoforms that are assembled. | |
| Library type | Specifies RNA-Seq protocol. | Standart Illumina |
| Mask file | Ignore all reads that could have come from transcripts in this file. It is recommended to include any annotated rRNA, mitochondrial transcripts other abundant transcripts you wish to ignore in your analysis in this file. Due to variable efficiency of mRNA enrichment methods and rRNA depletion kits, masking these transcripts often improves the overall robustness of transcript abundance estimates. | |
| Multi-read correct | Tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome. | False |
| Min isoform fraction | After calculating isoform abundance for a gene, Cufflinks filters out transcripts that it believes are very low abundance, because isoforms expressed at extremely low levels often cannot reliably be assembled, and may even be artifacts of incompletely spliced precursors of processed transcripts. This parameter is also used to filter out introns that have far fewer spliced alignments supporting them. | 0.1 |
| Frag bias correct | Providing Cufflinks with a multifasta file via this option instructs it to run the bias detection and correction algorithm which can significantly improve accuracy of transcript abundance estimates. | |
| Pre-mRNA fraction | Some RNA-Seq protocols produce a significant amount of reads that originate from incompletely spliced transcripts, and these reads can confound the assembly of fully spliced mRNAs. Cufflinks uses this parameter to filter out alignments that lie within the intronic intervals implied by the spliced alignments. The minimum depth of coverage in the intronic region covered by the alignment is divided by the number of spliced reads, and if the result is lower than this parameter value, the intronic alignments are ignored. | 0.15 |
| Cufflinks tool path | The path to the Cufflinks external tool in UGENE. | default |
| Temporary directory | The directory for temporary files. | default |
Parameters in Schema File
Type: cufflinks
| Parameter | Parameter in the GUI | Type | ||
|---|---|---|---|---|
| outputout-dir | Output directory | string | ||
| fileref-namesannotation | NameReference annotation | string | ||
| wigglerabt-outputannotationWiggle output | RABT annotation | booleanstring | ||
| wigglelibrary-spacetypeWiggle space | Library type | numeric | ||
| genomemask-size | Genome size (Mbp) | numeric | ||
| p-value | P-value | numeric | ||
| tag-size | Tag size (optional) | numeric | ||
| keep-duplicates | Keep duplicates | string | ||
| use-model | Use model | boolean | ||
| model-fold | Model fold | string | ||
| shift-size | Shift size | numeric | ||
| band-width | Band width | numeric | ||
| use-lambda | Use lambda | boolean | ||
| small-nearby | Small nearby region | numeric | ||
| large-nearby | Large nearby region | numeric | ||
| auto_bimodal | Auto bimodal | boolean | ||
| scale_large | Scale to large | booleanfile | Mask file | string |
| multi-read-correct | Multi-read correct | boolean | ||
| min-isoform-fraction | Min isoform fraction | numeric | ||
| frag-bias-correct | Frag bias correct | string | ||
| pre-mrna-fraction | Pre-mRNA fraction | numeric | ||
| path | Cufflinks tool path | string | ||
| tmp-dir | Temporary directory | string |
Input/Output Ports
The element has 1 input port:
Name in GUI: MACS data Input reads
Name in Schema File: in-dataassembly
Slots:
| Slot In GUI | Slot in Schema File | Type | ||
|---|---|---|---|---|
| Treatment features | _treatment-ann | ann-table-list | ||
| Control features | control-ann | ann-table-listAssembly data | assembly | assembly |
| Source url | url | string |
And 1 output port:
Name in GUI: MACS output data Output annotations
Name in Schema File: out-dataannotations
Slots:
| Slot In GUI | Slot in Schema File | Type | ||
|---|---|---|---|---|
| Peak regions | peak-regions | ann-table-list | ||
| Peak summits | peak-summits | ann-table-list | ||
| Treatment fragments pileup | wiggle-treat | stringIsoform-level expression values | isolevel.slot | ann_table |