jvarkit

TSSEnrichment

Transcription Start Site (TSS) Enrichment Score calculation

Usage

Usage: java -jar dist/tssenrich.jar  [options] Files
Usage: tssenrich [options] Files
  Options:
    --bins
      in the graphical output, normalize coverage over TSS using 'x' regions
      Default: 100
    --contig-regex
      use contigs matching this regex
      Default: (chr)?[0-9XY]+
    --extend, -x
      extend tss site by 'x' bases.A distance specified as a positive 
      integer.Commas are removed. The following suffixes are interpreted : 
      b,bp,k,kb,m,mb,g,gb 
      Default: 2000
    --gtf, -gtf
      GFF file to be used as a source of TSS start sites
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --mapq
      min mapping quality
      Default: 1
    -o, --output
      Output file. Optional . Default: stdout
  * -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard/gatk CreateSequenceDictionary or samtools dict
    --strand
      use strand TSS information to swap the before/after position of the read 
      according to the TSS strand.
      Default: false
    --threads
      number of parallel jobs
      Default: 1
    --treshold
      comma separated tresholds to set a status concerning,acceptable/ideal 
      see https://www.encodeproject.org/atac-seq/#standards
      Default: 6,10
    --use-transcript
      use 'transcript' type in GTF instead of 'gene'
      Default: false
    --version
      print version and exit

Keywords

• bam
• atacseq
• peak
• tss

Compilation

Requirements / Dependencies

• java compiler SDK 11. Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew tssenrich

The java jar file will be installed in the dist directory.

Creation Date

20240130

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/tss/TSSEnrichment.java

Contribute

• Issue Tracker: http://github.com/lindenb/jvarkit/issues
• Source Code: http://github.com/lindenb/jvarkit

License

The project is licensed under the MIT license.

Citing

Should you cite tssenrich ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030

Transcription Start Site (TSS) Enrichment Score

https://www.encodeproject.org/data-standards/terms/#enrichment

The TSS enrichment calculation is a signal to noise calculation. The reads around a reference set of TSSs are collected to form an aggregate distribution of reads centered on the TSSs and extending to 2000 bp in either direction (for a total of 4000bp). This distribution is then normalized by taking the average read depth in the 100 bps at each of the end flanks of the distribution (for a total of 200bp of averaged data) and calculating a fold change at each position over that average read depth. This means that the flanks should start at 1, and if there is high read signal at transcription start sites (highly open regions of the genome) there should be an increase in signal up to a peak in the middle.

Example

find /path -type f -name "*.bam" > bams.list
java -jar dist/jvarkit.jar tssenrich -R ref.fa --gtf jeter.gtf bams.list > output.txt

Output

output is a multipart text file. Each part can be isolated using awk. For example the following commands plot the normalized peaks using R

$ awk '$1=="NORMALIZED"' output.txt | cut -f 2- > jeter.txt
$ awk '$1=="R_PLOT"' output.txt  | cut -f 2-  | sed 's/__INPUT__/jeter.txt/;s/__OUTPUT__/jeter.svg/' > jeter.R
$ R --vanilla < jeter.R

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