Question: GMAP download page
0
gravatar for  DataFanatic
2.0 years ago by
DataFanatic260
DataFanatic260 wrote:

I am interested in analyzing PacBio long read (full transcript) RNAseq data using GMAP; however, GMAP download page seems to have been removed. Does anyone know if GMAP is still available for download? PacBio have their own software SMRTlink software but I believe this will not run on windows or mac but only on Unix systems. Can anyone confirm this???

pacbio rna-seq gmap • 777 views
ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by DataFanatic260
1
gravatar for Carambakaracho
2.0 years ago by
Carambakaracho2.2k
Germany/Cologne
Carambakaracho2.2k wrote:

In case GMAT is a typo, GMAP and GSNAP can be found here:

http://research-pub.gene.com/gmap/

The PacBio SMRTLink suite runs perfectly fine on Linux, i believe it even requires Linux

https://www.pacb.com/support/software-downloads/

ADD COMMENTlink written 2.0 years ago by Carambakaracho2.2k

Thank you for your answer, Yes I am referring to GMAP. Let me clarify my second question: I only have a PC/Mac and no Unix server. Can I install SMRTLink on my Mac/PC??

Also, is GMAP a good alternative to SMRTLink? I need to detect gene isoforms without a reference.

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by DataFanatic260
1

GMAP is only an alignment program where as SMRTlink is a suite of tools for working with PacBio data.

While official SMRTlink documentation clearly says this

SMRT Link server software cannot be installed on macOS® or Windows® systems.

You may be able to install SMRTlink on a Mac but it may not be worth the effort.

You should also look into minimap2 as an alternative alignment program.

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by genomax90k
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