total stranded fusion

Mp

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Nov 23, 2015, 4:47:05 PM11/23/15

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Hi!!
If I use reversed way as suggested in this link https://groups.google.com/forum/#!topic/rna-star/KZpu91GS-FA
I'm not able to detect any fusion! Could you help me o understand strand use on STAR?
What means this ?

For example, for the dUTP protocol, it's better to reverse the order of input reads, i.e. use --readFilesIn Read2 Read1. This will make the chimeric output order to follow the order on the RNA molecules

How appear on chimeric junction file?
thanks!

Alexander Dobin

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Nov 24, 2015, 11:39:44 AM11/24/15

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Hi Maurizio,

are you using STAR-Fuison, or just looking at the Chimeric.out.* files?

Cheers

Alex

Mp

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Nov 24, 2015, 4:09:04 PM11/24/15

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I'm looking the chimeric.out files. I'm interesting to learn more about that!!
thanks!!

Alexander Dobin

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Nov 25, 2015, 4:17:05 PM11/25/15

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Hi Maurizio,

are you saying that if you map --readFilesIn Read1.fastq Read2.fastq, you see chimeric output, but if you map with reversed mates, --readFilesIn Read2.fastq Read1.fastq, there is no chimeras detected?

This should not happen, only the strand of the alignments should revert, and there might be small changes in a very small % of mappings.

If you can send me a minimalistic example of this problem, I will check it.

Cheers

Alex

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