Question: MACE (Massive analysis of cDNA ends)
gravatar for Philippe
2.1 years ago by
Germany / Freiburg / Albert-Ludwigs-Universität
Philippe10 wrote:


does anybody have experience in doing downstream analysis on data created by the MACE-technology (Massive Analysis of cDNA ends)?

What are important differences compared to a regular analysis of mRNA or miRNA?

I know, it´s kind of a wide, non-precise question, but I just started working on that kind of data and I´m kind of lost.

Any kind of helpful advise would be much appreciated.



rna-seq galaxy • 783 views
ADD COMMENTlink modified 2.1 years ago by Mo Heydarian830 • written 2.1 years ago by Philippe10
gravatar for Mo Heydarian
2.1 years ago by
Mo Heydarian830
United States
Mo Heydarian830 wrote:

Hi Philippe,

I'm not super familiar with this RNA sequencing strategy, but from looking at this paper ( 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

Hope this helps!

Cheers, Mo Heydarian, Galaxy Team

ADD COMMENTlink written 2.1 years ago by Mo Heydarian830

Cheers for your response Mo!

This is the paper I also found while checking pubmed. I´ll try the procedures you mentioned.

Have a nice one.

Regards, Philippe

ADD REPLYlink written 2.1 years ago by Philippe10
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