SLaP

SLaP mapper (Spliced-Leader and Polyadenlyation site) mapper is a fully automated web-service for identification, quantification and gene-assignment of both spliced-leader and polyadenylation addition sites in Kinetoplastid genomes. SLaP mapper only requires raw read data and can use read data from Illumina or Ion Torrent RNAseq (single or paired end) and performs all read processing, mapping, quality control, quantification, and analysis in a fully automated pipeline.

UPDATE: SLaP mapper now accepts single end reads and reads from Ion Torrent sequencing. To analyse single end reads just upload one file as read file 1 below.

Genome Versions:

SLaP mapper is currently configured to use TriTrypDB genome release version 6.0. More genomes can be added upon request.

File upload requirements:

To speed up transfer of files, SLaP mapper only accepts read files in gzipped fastq format (e.g. read1.fq.gz). Due to FTP limitations SLaP mapper can currently only accept individual files less than 2GB. If your read files are larger then that then please split them into pieces each smaller than 2GB. Uploading uncompressed read files will cause the pipeline to fail.

Select your settings and upload your read files here:

Select species from which RNAseq was obtained:

Select minimum acceptable spliced-leader length:

Select minimum acceptable poly(A) length:

Enable filtering for false positive polyA sites:

Select read file 1:

Select read file 2:

Your e-mail address:*

*SLaP mapper can take a long time to run, results will be emailed to you when complete. Your e-mail address, read files and results are not stored on the server.

Example data:

Example data with which you can test SLaP mapper is provided here. There are two files: File 1 and File 2. The data is from a T15VN primed RNAseq experiment with Trypanosoma brucei. If you just wish to view a typical result package, the results generated from the example dataset can be downloaded from here.

If you use SLaP mapper please cite:

Fiebig, M., Gluenz, E., Carrington, M., and Kelly, S. (2014). SLaP mapper: A webserver for identifying and quantifying spliced-leader addition and polyadenylation site usage in kinetoplastid genomes. Molecular and Biochemical Parasitology – PDF