How is the Chimeric.out.junction when two of the paired end mates are chimeric?

[Jun Cheng]

He Alex,

thanks for the nice mapping tool STAR, and the Chimeric.out.junction output which makes further processing much easier.

I'm wondering how is the Chimeric.out.junction output be, when two of the paired end mates are both chimerically mapped. As far as I get, this is not able to be shown in one line as it usually does. 

Best regards,

Jun 

[Alexander Dobin]

Hi Jun,

are you asking about two different chimeric junctions in each of the mates? STAR does not output such junctions, it only allows one chimeric junctions per single- or paired-end read.

In principle, you can map the reads separately - then STAR will detect possible junctions in each of the mates - and combine the two mates manually.

Cheers

Alex

[Jun Cheng]

Hi Alex,

sorry to bring this old question again. Are you planning to include multiple chimeric junctions in one read (pair) into the Chimeric sam or chimeric.out.junction file, or any other output file? Because the sequencing length is increasing, and it is very likely that in one long read (pair) there are multiple chimeric junctions.

Best wishes,

Jun

[Alexander Dobin]

Hi Jun,

I agree that it would be a useful feature, and have it in my plans - however, it will require complete re-working of the chimeric routine, since the 2-segment detection is hard-coded. 

Unfortunately, I cannot give you a realistic ETA on this feature.

Cheers

Alex