Figure S12. Validation of 3'UTRs using RNA-Seq data
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Figure S12. Validation of 3'UTRs using RNA-Seq data
Blast. Number Of reads aligned. 407424 reads aligned to genome. (62%). Used only poly A/T reads. 0. 7. 14. 21. 28. 35. 42. 49. 56. 63. 70 ï ï ï ï ! Read Length. P.
Coverage_Upstream - Coverage_Downstream
A
PC: 4-50
50-100
Bin1
Bin2
100-200 Bin3
200-300
300-500
Bin4
Bin5
B
> 500
Raw Numbers
Percentage
432
100
111
25.6
With Evidence
84
19.4
Remaining
27
6.25
Bin6
20
Total candidates Outliers 15
10
IN-OUT
5
*PC: Peak coverage 0
C
Processing Ion Torrent Reads
D variable Percentage of Reads
Raw Reads 2353375 (2 M)
Filter 1: Trimming Poly A’s & Poly T’s *Reads with poly A’s are trimmed off. *Reads with poly T’s are trimmed & reverse complemented
Filter 2: Length filter >30nt
Processed Reads: Used only 662095 reads poly A/T reads considered as 100% Number Of reads aligned
21341
377909
Bowtie2
8174
Blast
Reads are aligned to genome using bowtie2 & blast.
ï
AfterAlignment
ï
ï
ï
!
Read Length
E
Coverage_upstream - Coverage_downstream
Reads with A at the end : 366259 (16%). Reads with T’s at the end: 295836 (12.6%).
BeforeAlignment
70 63 56 49 42 35 28 21 14 7 0
20 40
15 10
20 5 0
0
í
51$í6HT
,RQíWRUUHQW
407424 reads aligned to genome. (62%).
Figure S12. Validation of 3’UTRs using RNA-Seq data. A) RNASeq coverage for upstream region (from transcript end to polyadenylation site start) and downstream region (after polyadenylation site) across different bins of polyadenylation site coverage (PC). The difference in the RNA-Seq coverage values in the upstream and the downstream region increases with the increase in PC. B) Table depicting raw number and percentage of transcripts used in validation of 3P-Seq using RNA-Seq data analysis. C) The schematic describing the different steps of pre-processing for reads obtained from Ion torrent platform. D) The binned-frequency of the Ion-torrent read lengths. More than 80% of reads have > 100nts. E) A violin plot depicting the difference in the coverage between the upstream and downstream region derived from RNA-Seq and Ion-Torrent reads.
