2.1 years ago by
I'm not super familiar with this RNA sequencing strategy, but from looking at this paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3928179/) it seems like MACE is a strategy for specifically sequencing the 3' ends of RNA transcripts. The libraries will have a large polyA stretches within the reads (oligo-dT is used to prime the reverse transcriptase), so you would need to perform a clipping/trimming step prior to alignment and subsequent abundance estimation.
For trimming the polyA stretches, have a look at the tools: Clip, Trimmomatic, Manipulate FASTQ, and Trim Galore, these are under the NGS: QC and manipulation category. For alignment you should use Tophat or HISAT, these tools can deal with mapping spliced reads if you capture splice junctions in your MACE library. To quantify abundance estimates you could use Cuffdiff or HTseq-count with DEseq2. These tools are all available on useGalaxy.org.
Hope this helps!
Mo Heydarian, Galaxy Team