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Significance of column 'strand' and 'max splice overhang' in STAR output

Hello,

I have paired end Illumina data (150 bps). I used STAR and I am interested in identifying novel splice junctions.

I am having trouble understanding the significance of 2 columns in the SJ.out.tab file and would really appreciate your help with understanding -

What is the need and significance of -

  1. Column 4 - Strand
  2. Column 9 - max splice overhang.

Thank you so much!

rna-seq star splicing
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updated by Ram Ram • written by snishtala03 • snishtala03

1 answer

Strand is the DNA strand the transcript is derived from. DNA is double stranded, and RNA is transcribed from one of the strands.

As for your second question, if you had googled "splice junction overhang", you'd have seen this previous post

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written by Ram Ram

I did come across that post. It says max splice overhang basically tells the most confident spliced read. I was hoping if I could understand a little more about the importance of this column.

I know what a Strand is. I am more interested in knowing why information about a junction from positive or negative strand is important?

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written by snishtala03 • snishtala03

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