Question: Question about hisat2 parameter "--no-templatelen-adjustment"
gravatar for ChrisT
8 months ago by
ChrisT0 wrote:


I am quite new at analysing NGS data, but I am trying to set up a pipeline for my lab. We have performed single end sequencing using Ion Torrent Proton to analyse differential gene expression (through QuantSeq 3' mRNA-seq). I am testing alignment using the Hisat2 aligner, however I am not sure whether I need to use the parameter --no-templatelen-adjustment. I read the manual and paper describing the aligner, but it is not quite clear for me what this parameter does exactly. Can anyone help?

Thank you in advance.

rna-seq alignment • 271 views
ADD COMMENTlink written 8 months ago by ChrisT0

I would say it is not totally clear for me neither

Samtools definition of TLEN :

If all segments are mapped to the same reference, the unsigned observed template length equals the number of bases from the leftmost mapped base to the rightmost mapped base.


Disables template length adjustment for RNA-seq reads.

In your case as you're working with single end, I think that the size of the template is equal to the size of your read

I do not know the effects of disabling the template length adjustment

But in any case if you don't understand an option, do not use it

Some info :

Edit :

Template length adjustment for RNA-seq reads is used to fit TLEN to the transcript length template due to splicing events

Using the --no-templatelen-adjustment you will got a template length based on the reference sequence (which in not what you want in typical RNA-Seq analysis).

But some tools as Manta (issue above) needs this template length information to the reference.

In conclusion, do not use it

ADD REPLYlink modified 8 months ago • written 8 months ago by Bastien HervĂ©4.4k

Thank you very much for your help!

ADD REPLYlink written 8 months ago by ChrisT0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1161 users visited in the last hour