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Maximum spliced alignment overhang in STAR output

Hi hello, I am working with STAR and I 'am looking at the SPLICE JUNCTION (SJ.out.tab) output, I do not understand the meaning of the column line 9: maximum spliced alignment overhang

Column 9: maximum spliced alignment overhang

I compute the distribution of the column 9 values for reads of 100 bp, getting ranges from 50 to 12:

311 50
340 49
292 48
266 47
 --------
196 14
263 13
355 12

So I am not sure what this number means. I was expecting to get the value 50 as a minimum and maximum of 99....Can someone explain to me the real meaning of this column???!

THANKS!

alignment splice junctions star alignment overhang
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updated by Jeffin Rockey Jeffin Rockey • written by sradio91 • sradio91

1 answer

There is an explanation from STAR author in a related discussion here. Hope it helps.

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written by Jeffin Rockey Jeffin Rockey

Thank you very much Jeffin, that is the answer that I was looking for!

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written by sradio91 • sradio91

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