Question: HISAT2 relaxing parameters?
0
gravatar for biogirl04
2.4 years ago by
biogirl040
biogirl040 wrote:

Hi,

It's my first time using HISAT2 and the options have gotten me all confused. How can I run HISAT2 such that I increase the number of mapped reads by relaxing the parameters? Essentially, how can I increase the number of mismatches, etc allowed (which options do I need to use and how)?

Thanks so much!

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by biogirl040
1

From your other thread ( Tophat2 Error gzip pipe broken? zipped file empty? ), I see an unusual pattern for NGS datasets, which usually consists of millions of short reads:

left reads: min. length=75, max. length=10506, 15483 kept reads (0 discarded)

So this clearly is not raw Illumina, Ion Torrent or 454 data. Are you still aligning the same dataset? What is the source of this data? Are these assembled transcripts, or PacBio reads?

ADD REPLYlink written 2.4 years ago by h.mon31k

Oops, sorry I didn't clarify this before. This is Oxford Nanopore Sequencing data.

ADD REPLYlink written 2.4 years ago by biogirl040
2

Go with minimap2, which seems to be the current go-to tool for Nanopore data. It is optionally splice-aware.

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by ATpoint41k

... that's quite crucial to mention and may explain some results from other aligners :-)

I agree with ATpoint, use minimap2.

ADD REPLYlink written 2.4 years ago by WouterDeCoster44k

As a general rule of thumb for the majority of the tools, if you don't know which parameters to set: stick to the defaults and trust the judgement of the developers.

ADD REPLYlink written 2.4 years ago by WouterDeCoster44k

Hi,

Yes, I understand that. However, I am using the default and am not getting what I expected. I just switched from using tophat2 to hisat2 and I know that hisat2 is much more sensitive. Is there a similar option on hisat2 to change the --read-mismatches, --read-edit-dist, and --read-gap-length?

Thanks!

ADD REPLYlink written 2.4 years ago by biogirl040
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