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Question: difference between tophat2 and tophat for illumina
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gravatar for ajmaninisha
3.7 years ago by
ajmaninisha • 30
Canada
ajmaninisha • 30 wrote:

Hi 

I have paired end read and am confused i should tophat 2 or tophat for illumina. What is the difference between the two. And why should we choose Tophat2 or Tophat for Illumina.

Also, i have genome and annotation file which is in asn file format not in gff format. Will galaxy automatically convert into gff format or readable format accepted by the galaxy.

Kindly advise
tophat2 tophat gtf mapping • 1.4k views
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modified 3.7 years ago by Bjoern Gruening ♦ 5.1k • written 3.7 years ago by ajmaninisha • 30
1
gravatar for Bjoern Gruening
3.7 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

Hi,

`Tophat for Illumina` is an older version of Tophat and you should use Tophat2. As far as I know the conversion from ASN and GFF is not straightforward. If you can try to find a GFF or GTF file.

 

Hope this helps,

Bjoern
ADD COMMENT • link written 3.7 years ago by Bjoern Gruening ♦ 5.1k
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