Understanding read_distribution.py output

[Nikelle Petrillo]

Hello, 

Here is my output from read_distribution.py. How do I tell how many reads were aligned to intergenic regions?

Thanks!

Total Reads                   953788

Total Tags                    1904659

Total Assigned Tags           1901367

=====================================================================

Group               Total_bases         Tag_count           Tags/Kb

CDS_Exons           473135427           1869127             3.95

5'UTR_Exons         0                   0                   0.00

3'UTR_Exons         0                   0                   0.00

Introns             135818819           31536               0.23

TSS_up_1kb          243617661           393                 0.00

TSS_up_5kb          557269214           450                 0.00

TSS_up_10kb         752561269           450                 0.00

TES_down_1kb        241521496           245                 0.00

TES_down_5kb        545416383           254                 0.00

TES_down_10kb       732467317           254                 0.00

=====================================================================

[Liguo Wang]

subtract tags mapped to (CDS_Exons  + 5'UTR_Exons + 3'UTR_Exons + Introns) from "Total Assigned Tags".

Liguo

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[Nikelle Petrillo]

Thanks! Also, is there a reason why it looks as if no reads are aligning to either the 5' or 3' UTR exons?

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[Liguo Wang]

Sorry for late reply. It's probably because 3' and 5' UTR were not defined in you BED file.  Check your BED file, if coordinates in column2 and column7 are the same (and coordinates in column3 and column8 are the same),  your BED file only defines exons but does not distinguish UTR exons and CDS exons.

Liguo

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