Improving the RNA–Seq precision with MapAl
Online Supplement

MapAl is a tool for RNA-Seq expression profiling that builds on the established programs Bowtie and Cufflinks.
Allowing an incorporation of ‘gene models’ already at the alignment stage almost doubles the number of transcripts that can be measured reliably.

MapAl usage:

Synopsis: perl -i input_file -g GTF_file [-t temp_path] [-s mem_size] [-S strandedness] [-P pair_orientation] [-o output_file]

When -S and -P parameters are specyfied MapAl will filter out all alignments which do not fulfill specified strand orientation requirements. Orientation of alignment is assesed by examining the FLAG field (SAM format) of the input file.

MapAl is available under the GPL. You can download the stand-alone MapAl script.

All versions of MapAl are available here

MapAl package:

The MapAl package contains the components of the MapAl pipeline together with appropriate test data: download the MapAl package (70MB).

The package contains:

TopHat package:

For a comparison we also provide a package where the well established tool TopHat is used with the corresponding test data: download the TopHat package (130MB).

The package contains: The TopHat pipeline produces two output sets: The second of these sets can be combined with results from the MapAl pipeline for comprehensive profiling with increased precision.

For testing purposes Bowtie v0.12.7, TopHat v1.1.4, and Cuffflinks v0.9.1 were used. Newer versions should work as drop-in replacements as long as they are backwards-compatible. Note that these tools may have their own depencies that need to be installed.

In order to adapt the pipeline scripts to different data set types, corresponding appropriate changes in the Bowtie, TopHat, and Cuffflinks execution options may be required.

The SEQanswers forum is a good place to look for advice after having read the available documentation.

If you have any further question to MapAl authors please contact us.

If you would like to know more about our group please visit our homepage.

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