Fish the ChIPs

Configuration file

Complete the form on the right with the values of all the desired parameters and then click the download button to get the corresponding configuration text file.

Moving the mouse pointer over the name of most of the parameters shows you a small popup reporting useful details.

Steps of the analysis

Specify which steps to include in the analysis.

  Raw files conversion  
  Quality Control  
  Alignment  
  Peaks finding  
  Peaks annotation  
  BigWig files  
  TDF files  
  FC directory  
  Working directory  
 
 

Species

  Species                    
 
 

Samples

Here you can specify as many samples as you like. For each one of them, you can choose the name you prefer (just be careful avoiding full stops and special chars). Besides, for each sample you must specify the path of the corresponding SRF raw file(s). If you have more than one srf file for a certain sample, you have to list all of them separated by commas. If you are skipping some steps, you still must specify here the names of your fastq files or even of the processed files, just remember to replace any file extension with .srf to make the pipeline works properly..

Click the Add button if you need more samples.

   
 
 

Comparisons

Here you can specify every single pairwise comparison the pipeline is going to perform.

Click the Add button if you need more comparisons.

   
 
 

Raw files conversion

Here you can specify all the parameters for the raw files conversion.

Expand Customize parameters
  Filter low quality reads  
  srf2fastq name and path  
  fastq-dump name and path  
 
 

Quality Control

Here you can specify all the parameters for the quality control check.

Expand Customize parameters
  Program name and path  
 
 

Bowtie parameters

Here you can specify all the parameters for the alignment of your short reads.

Expand Customize parameters
  Alignment Mode  
  Max num. of mismatches (-v)  
  Alignment suppression (-m)  
  Max "seed" mismatches (-n)  
  Seed length (-l)  
  Max tot. quality values (-e)  
  Trim bases before align. (-3)  
  Input qualities (-quals)  
  Use colorspace index (-C)  
  Number of CPU (-p)  
  Best mode (--best)  
  Seed for random (--seed)  
  Output format  
  Program name and path  
  Index path
  Custom parameter  
 
 

MACS parameters

Here you can specify all the parameters for the peak calling steps.

Tag size (s)  
Expand Customize parameters
  Effective genome size (g)   h.sapiens m.musculus c.elegans fruit fly
  MFOLD range for model (m)   min.   max.
  Pvalue cutoff (p)  
  Band width (bw)  
  Arbitrary shift size (-shiftsize)  
  Format of tag file (f)  
  Local lambda (-nolambda)  
  Shifting model (-nomodel)  
  Create Wig files  
  Wig resolution (--space)  
  Program name and path  
  Custom parameter  
 
 

GIN parameters

Here you can specify all the detais regarding the annotation using genomic features from your reference genome.

Priority
 
Promoter definition
 
Expand Customize parameters
  Annotation table and path  
  Program name and path  
 
 

Merge parameters

Here you just have to specify the complete path of the merge.py script on you machine. This script simply merge the results from MACS with the genomic annotation coming from GIN in order to provide you with a single table containing all the information.

Expand Customize parameters
  Program name and path  
 
 

PIES_PEAKS_GD parameters

Here you just have to specify the complete path of the PIES_PEKAS_GD script on you machine. This script generates pie charts for the genomic annotations coming from GIN.

Expand Customize parameters
  Promoter definition
 
  Program name and path
 
 
 

TSS_3UTR_DIST parameters

Here you can specify all the parameters for TSS_3UTR_DIST. Besides the complete path of the TSS_3UTR_DIST on your computer, you must specify the BED table with the coordinates of the genes on which the script annotates your regions.

Expand Customize parameters
  Table name and path  
  Program name and path  
 
 

wigToBigWig parameters

Here you just have to specify the complete path of the wigToBigWig executable and of the file that lists the lengths of the chromosomes of the reference genome you aligned your short reads.

Expand Customize parameters
  Program name and path  
  Chrom lengths file and path  
 
 

IGVTools parameters

Here you just have to specify the complete path of the IGVTool executable and its genome file.

Expand Customize parameters
  IGVTools name and path  
  IGVTools genome file path