Mapping parameters

[Renana]

Hi!

Did you perform a size selection on mRNA reads for the mRNA-seq coverage plot mapping?

Some of the mapping information appears in the forum (A-site assignment in ribosome profiles for example) but I'm not sure where to look for mRNA-seq mapping information. Is it possible to view the parameters used for the mRNA-seq mapping (size of reads, bowtie parameters, etc..)?

many thanks!

[jamespa]

Hi Renana,
we use 25 for the seed length parameter (--seedlen) for Bowtie. I'll let you know other details next week when I'm back in the office.
Regards
jamesp

[audrey]

Hi Renana,

The mRNA-seq reads can vary in length from study to study. For GWIPS-viz mRNA-seq coverage profiles, the only restriction for the mRNA-seq reads alignment is that they are of minimum length 25 nts (after the removal of the adapter sequence).

If you have further questions related to this, please let us know.

Audrey