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foerstner-lab / READemption

A pipeline for the computational evaluation of RNA-Seq data
https://reademption.readthedocs.io
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Does v0.4.5 support using STAR as aligner ? #12

Closed altairwei closed 5 years ago

altairwei commented 5 years ago

I looked through the source code of READemption, and found some flags in bin/reademption : 

    read_aligning_parser.add_argument(
        "--STAR_bin", default="STAR",
        help="STAR's binary path (default 'STAR').")

So, I guess that v0.4.5~v0.4.x would support STAR, is that right ?

I'm really not familiar with segemehl and cannot distinguish the differences between segemehl and STAR/HISAT2 .

I'm glad to hearing this news. Thank you !

Tillsa commented 5 years ago

Using STAR with READemption is still under development and hasn't been tested yet. That's why I would recommend using segemehl right now. segemehl is slower than STAR but the mapping accuracy is similar. You can checkout this page where different mappers are being compared: http://www.ecseq.com/support/benchmark.html.

altairwei commented 5 years ago

Using STAR with READemption is still under development and hasn't been tested yet. That's why I would recommend using segemehl right now. segemehl is slower than STAR but the mapping accuracy is similar. You can checkout this page where different mappers are being compared: http://www.ecseq.com/support/benchmark.html.

Thank you very much !