Tophat with mm10 gencode

Question

[dec986]

Hello,

I am attempting to use gencode M6 (http://www.gencodegenes.org/mouse_releases/current.html) to align with tophat, but this fails.

I make the bowtie alignment:

time bowtie-build Mus_musculus.GRCm38.dna_sm.toplevel.fa mm10

and this generates 6 files with .ebwt suffixes, which I renamed to .bt2:

mm10.1.bt2  mm10.2.bt2  mm10.3.bt2  mm10.4.bt2 mm10.rev.1.bt2  mm10.rev.2.bt2

The tophat command is almost identical to what I ran with the refSeq genes:

tophat -G /home/con/.GENE_DATA/gencode.vM6.annotation.gtf -p 8 ~/.GENE_DATA/mm10 /home/con/EctoPlacentalCone/11-4-D2_2/11-4-D2_2.fq

but this fails. How can I run tophat with gencode?

Thanks,
DEC

[Martombo]

You have to use bowtie2-build

Answer 1

[GouthamAtla]

As said before, you should use bowtie2-build. Renaming the file extension does not help. Or keep the original file extensions as it was before and use --bowtie1 option with tophat2, tophat2 will use bowtie1 instead of bowtie2.