QoRTs/JunctionSeq with Rsubread alignment

[jmbono]

Hi,
I apologize if this is not the most appropriate place to ask this question, but I tried to post on the Bioconductor forum, but it wouldn't allow me because QoRTs and/or JunctionSeq were not on the package list (I also noticed it says JunctionSeq is deprectated?). Here is the question I was attempting to post--any insight would be greatly appreciated, and, again, I apologize if this is not the best place to ask these sorts of questions:

I am interested in using QoRTs/JunctionSeq to analyze a dataset and I have reads aligned using the subjunc function in Rsubread. After reading the QoRTs/JunctionSeq manuals, I am unsure what to enter for the minMAPQ parameter as there is no suggested value given for Rsubread. I was unable to find any information regarding the MAPQ score from Rsubread documentation. My question is whether I should just use the default setting, or something else, or whether I just shouldn't try to use QoRTs/JunctionSeq on files aligned with Rsubread since I don't know what MAPQ convention it uses? Thank you very much for any insight you can provide.

[hartleys]

I would just shut off the mapq filter by setting minmapq to zero. Some aligners use mapq. Some do not. If they don't then don't filter on mapq.

…

On Tue, Mar 16, 2021, 1:20 PM jmbono ***@***.***> wrote: Hi, I apologize if this is not the most appropriate place to ask this question, but I tried to post on the Bioconductor forum, but it wouldn't allow me because QoRTs and/or JunctionSeq were not on the package list (I also noticed it says JunctionSeq is deprectated?). Here is the question I was attempting to post--any insight would be greatly appreciated, and, again, I apologize if this is not the best place to ask these sorts of questions: I am interested in using QoRTs/JunctionSeq to analyze a dataset and I have reads aligned using the subjunc function in Rsubread. After reading the QoRTs/JunctionSeq manuals, I am unsure what to enter for the minMAPQ parameter as there is no suggested value given for Rsubread. I was unable to find any information regarding the MAPQ score from Rsubread documentation. My question is whether I should just use the default setting, or something else, or whether I just shouldn't try to use QoRTs/JunctionSeq on files aligned with Rsubread since I don't know what MAPQ convention it uses? Thank you very much for any insight you can provide. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#58>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAWC53BVCJNUUZ65TP6LRXDTD6HNTANCNFSM4ZI7GY3A> .

[jmbono]

Thank you!!