MAJIQ build intron offset

[Miriam Martínez]

Hi biociphers team,

after checking the MAJIQ process, I noticed that on the MAJIQ build step I get this line for some of my samples: "Intron offset X miscalculated" (being X different numbers on the samples). I have tried to look up some info for this message, but I couldn't find about it. If I could have some info about it and if it means that the MAJIQ build has some type of error? Thank you in advance.

Best regards,

Miriam Martínez

[Swethaa NG]

Hi,

Was this question answered in private? I have the exact same doubt and it would be useful to know how to tackle it. I can provide the command details if needed. Thanks!

Kind regards,

Swethaa

[San Jewell]

Hi All,

I believe one of the Majiq developers did respond in private, but as he has since left the lab, I've been having trouble contacting him about this specific message. What I do know is that this is data dependent and is only generated on a specific unexpected read case. It would help to be able to see the minimum set of data which generates the error, so that we can analyze exactly what's happening with these reads. Would you be opposed to sharing your input data over private channels to discuss this issue? You can reach out to sje...@pennmedicine.upenn.edu for private communications and we can resume here once there is a conclusive answer.

Thanks,

-San

[Miriam Martínez]

Hi all,

in the end, this question was never answered to me, so I continued with my analysis hoping this wasn't affecting to the results as I couldn't find any information about it. Right now I'm running a new analysis with new data and I'm facing the same problem. It would be awesome if we could discover what does these wanrnings mean. I'm open to help to try to find what's happening. I wrote San a private mail a few days ago about the data sharing. I hope that in the end we can get to the bottom of the issue and share an explanation/solution for it. I look foward to your response on the mail I've sent.

Best,

Miriam

[San Jewell]

Hi Miriam,

Please see my reply to the private email you sent regarding the data transfer.

Thanks,

-San