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Ashraful Arefeen
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README.md

TAPAS: Tool for Alternative Polyadenylation Site Analysis

Accoring to the central dogma of molecular biology, a pre-mRNA is synthesized from the coding sequence of a gene during the transcriptional process. This pre-mRNA is coverted into a (mature) mRNA by the post-transcriptional process. The post-transcriptional process consists of three major steps. One of them is the addition of polyadenylation (polyA) tail using the polyadenylation pocess, which in turn consists of two substeps: cleavage at the 3' end of the pre-mRNA and addition of a polyA tail at the cleavage site. But, due to the effect of certain cis-acting elements and trans-acting factors, alternative cleavage sites can be formed from in a pre-mRNA. More precisely, a single pre-mRNA may often produce more than one mRNA with 3' untranslated regions (3' UTRs) of different lengths. TAPAS is a tool for detecting such alternative (or all) polyadenylation (APA) sites within a gene from RNA-Seq data. If two biological samples with multiple replicates are given, TAPAS can indentify differentially expressed APA sites between the samples. Moreover, its differential analysis has been extended to discover the shortening/lengthening of 3' UTRs within a gene.

Requirements

  1. The tool runs on linux machine.

  2. samtools 1.3. In order to run samtools, htslib is needed. Therefore, please download both htslib-1.3.tar.bz2 and samtools-1.3.tar.bz2. First extract and install htslib and then samtools. Please run the following command to install htslib:

     ./configure
     make
     make install
    

    Please run the following command to install samtools:

     ./configure
     make
     make install
    
  3. R 3.1.3. After downloading and extracting the R version, please run the following command to install:

     ./configure
     make
    

    These are the original sites for samtools and R.

  4. matrixStats, locfit and stats packages of R (please run package_install.R script).

APA site detection

APA_sites_detection of TAPAS detects novel APA sites of genes.

USAGE

./APA_sites_detection {OPTIONS}

OPTIONS

-ref <annotation_file_name>	An annotation file is given using this option. 
				e.g. Human annotation file is given in Finding_APA_Sites directory for reference.

-cov <coverage_file_name>	A read coverage file is provided using this option.
				Samtools is used to have the read coverage.

-l <int>			Read length

-o <output_file_name>		Output file name is given using this option.

-p <double>			A penalty value can be provided using this option.
				If nothing is given, the value is determined from the 
				read coverage of the 3' UTR frame.

EXAMPLE

./APA_sites_detection -ref refFlat_sf.txt -cov coverage_read_50.txt -l 76 -o expression_with_cp_read_50.txt

Output of APA site detection

The output file consists of six columns: gene name, chromosome name, strand of the gene, detected APA sites, abundance of those APA sites, read count of those APA sites respectively.
Note: The abundance of each detected APA site = read count of the APA site / length of the 3' UTR (that contains the APA site)

Differential APA site analysis

Diff_APA_site_analysis of TAPAS does differential analyses between two biological samples.

USAGE

./Diff_APA_site_analysis {OPTIONS}

OPTIONS

-C1 <cond1_f1,cond1_f2,cond1_f3,..>	Comma separated file names of condition 1 are given using this option. Each of these files
					is the APA site detection file, outputted by the first part of TAPAS (outputted by APA_sites_detection).

-C2 <cond2_f1,cond2_f2,cond2_f3,..>	Comma separated file names of condition 2 are given using this option. Each of these files 
                                            is the APA site detection file, outputted by the first part of TAPAS (outputted by APA_sites_detection).

-a <annotation_file_name>		An annotation file is given using this option. This file is similar to the annotation file
					of the APA site detection analysis.

-cutoff	<int>				Cutoff value is given using this option. This parameter is explained in TAPAS manuscript.
					Default value: 70

-type	<d/s>				Type of differential analysis. d -> differential APA site analysis, s -> shortening/lengthening
					event analysis.

-o <output_file_name>			Ouput file name is given using this option. 
					Default: for differential APA site analysis "diff_result_final.txt", 
						for shortening/lengthening event analysis "decision_output.txt"

EXAMPLE

./Diff_APA_site_analysis -C1 cond1_r1.txt,cond1_r2.txt,cond1_r3.txt,cond1_r4.txt,cond1_r5.txt,cond1_r6.txt -C2 cond2_r1.txt,cond2_r2.txt,cond2_r3.txt,cond2_r4.txt,cond2_r5.txt,cond2_r6.txt -a refFlat_sf.txt -cutoff 70 -type s -o deci_output.txt

Output of differential analysis

For differential APA site analysis, the output file contains eight columns: chromosome name, gene name, strand, APA site, log2 fold change, p-value, adjusted p-value, decision.
For shortening/lengthening event analysis, the output file contains six columns: chromosome name, gene name, strand, shorter APA site, longer APA site, log2 fold change. It also produces differentially expressed APA site file. This file contains eight columns: chromosome name, gene name, strand, APA site, fold change, log2 fold change, p-value, adjusted p-value. P-value is always adjusted using BH method.

Useful commands

How to calculate coverage using samtools

Command to calculate coverage from bam file:

samtools sort accepted_hits.bam -o sorted_accepted_hits.bam
samtools index -b sorted_accepted_hits.bam
samtools view -b sorted_accepted_hits.bam > accepted_reads.bam

samtools depth accepted_reads.bam > read_coverage.txt

Reference

  1. TAPAS: tool for alternative polyadenylation site analysis. Bioinformatics, 2018.
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