Does tophat allow indel mapping in reads?

[louis7781x]

Hi,

I know bowtie can't allow indel while mapping.

So,Does tophat also can't allow indel?


Because I think if aligner can't allow indel, a lot information of mutation may miss.

And If I want to do quantitation after alignment(like cufflink),it should be not perfect .

[Jon_Keats]

The new versions of Tophat support indels to an extent. See the current manual and look for the following flag "--allow-indels" by default it will allow up to 3 bp indels you can modify the allowed size.

[louis7781x]

The new versions of Tophat support indels to an extent. See the current manual and look for the following flag "--allow-indels" by default it will allow up to 3 bp indels you can modify the allowed size.

I see,Thanks!

[louis7781x]

The new versions of Tophat support indels to an extent. See the current manual and look for the following flag "--allow-indels" by default it will allow up to 3 bp indels you can modify the allowed size.

Hi, but non-splicing read also can't allow indel.Right?