Results¶
Results of the pipeline are presented in the form of table. Additionally the pipeline generates plots that can be used to immediate inspection of the results. The pipeline during run generates many files. You can check the files generated at each step in the Pipeline flow section.
The file with results is called test/results_with_probability_annotated.tab. This is an example of the table generated by the run of test:
RNA18S 1805 1806 snoID_0145 35.0 + -32.5 -2.362136710375476 T ((((((((((((((((((((.&)))))))))))))))))))) 0.9985874938860818 1806 NA NA NA NA NA
RNA28S 3722 3723 snoID_0051 297.0 + -24.5 -0.8262461258511468 G .((((((((((((((((.&.)))))))))))))))). 0.9820269187646468 3723 NA NA NA NA NA
RNA18S 461 462 snoID_0091 10.0 + -26.6 -2.0974042420540084 C ((((((((((((((.((.&.)).)))))))))))))) 0.9769660814617612 462 NA NA NA NA NA
RNA18S 1030 1031 snoID_0038 15.0 + -24.6 -1.5332765514685365 A (((((((((((((((((.&.))))))))))))))))) 0.9764776374727128 1031 NA NA NA NA NA
RNA28S 390 391 snoID_0128 638.0 + -22.6 -0.4628266825472744 A .(((((((((((((.&.))))))))))))). 0.9730740226153078 391 NA NA NA NA NA
RNA18S 1271 1272 snoID_0080 24.0 + -26.5 -3.0061575391125657 C .((((((((((((.&.)))))))))))). 0.9729293415188028 1272 NA NA NA NA NA
RNA18S 467 468 snoID_0114 6.0 + -25.5 -3.9820153772481808 A (((((((((((((((.&.))))))))))))))) 0.970629236316464 468 NA NA NA NA NA
RNA18S 461 462 snoID_0064 11.0 + -25.7 -2.040235979926924 C ((((((((((((((.&.)))))))))))))) 0.9680243404065784 462 NA NA NA NA NA
RNA18S 461 462 snoID_0094 18.0 + -25.7 -2.316104404986292 C ((((((((((((((.&.)))))))))))))) 0.9680243404065784 462 NA NA NA NA NA
RNA18S 461 462 snoID_0124 1.0 + -25.6 -2.2282206777051834 C ((((((((((((((.&.)))))))))))))) 0.9668440616572168 462 NA NA NA NA NA
Columns:
Column Number | Description |
---|---|
1 | Chromosome |
2 | Start (0-based) |
3 | End (1-based) |
4 | snoRNA ID |
5 | Chmieras count |
6 | Strand |
7 | Interaction energy (PLEXY) |
8 | Log site specificity |
9 | Modified nucleotide |
10 | Interaction structure (PLEXY) |
11 | Interaction probability from the model |
12 | Modification position (1-based) |
13 | Genecode gene type eg. protein_coding |
14 | ENSEMBL ID |
15 | Gene name |
16 | Transcrip region eg. intron |
17 | mRNA region eg. five_prime_UTR |
Note
Log site specificity feature is not used to calculate probability. It is calculated ad a ratio between number of chimeric reads for specific positions and snoRNA with total number of chimeric reads for particular position.
Inspection of a run¶
In order to quick inspect the run use plots produced by the pipeline.
Score histogram¶
As can bee seen in the figure scores for unshuffled reads are way highter than for shuffled ones. This indicates the enrichment of snoRNAs in reads.
Read profiles¶
One can also check the profile of the split chimeras that map to particular target RNA along its sequence.
In order to see previous 2’-O-methylation positions they should be declared in the snoRNA table.
It can be seen that the spots with known modifications are covered by more chimeric reads.
Probabilities¶
Another important plot produced by the pipeline are the probabilities derived from model ploted for each nucleotide in the target RNA.
It can be immediately seen that the positions with knwon modification sites have higher probability values. Which indicates that the experiment is working as expected.
RNAduplex¶
RNAduplex part of the pipeline also produces its own results table. This can be used to investigate non-canonical interactions. The table is called results_with_RNAduplex_score_annotated.tab:
RNA18S 103 153 snoID_0159 1 + 0.0 NaN NaN NaN NaN 0.0 82 0.426829268293 -28.20 -15.50 -24.10 ######################.((((((....((((((((((((((....(((((((..............(((((.#### 23,78 1,48 ###############.(((((.(((.(((.(((((((((....(((...............((((.(((((.### NA NA NA NA NA
RNA18S 141 191 snoID_0159 1 + -9.6 .(((((((((.&.))))))))). GGTAAmTTCTAG&ATAGGATTACG D 159 -8.9 82 0.426829268293 -20.60 -20.20 -22.10 ##########################.((((......(((.(((..(((........((((..(((((((((((.....((. 27,82 3,45 #########################.(((((((((((((((((.((((...((( NA NA NA NA NA
RNA18S 288 338 snoID_0159 1 + 0.0 NaN NaN NaN NaN 0.0 82 0.426829268293 -21.20 -27.90 -22.90 #######################.(((((((..(.(.((((...............(((.......((((...((((((.## 24,80 14,50 ################.((....(((((((.................((..(((..(((....((((((.((.## NA NA NA NA NA
RNA18S 1243 1293 snoID_0159 1 + 0.0 NaN NaN NaN NaN -4.8 82 0.426829268293 -22.20 -13.90 -24.40 #.((((((........(((.....(((((.(....(.(((((.......................((....((.((((.### 2,79 3,50 ################################################################.(((((...((((..(((.(((.(((.## NA NA NA NA NA
RNA18S 1255 1305 snoID_0159 1 + 0.0 NaN NaN NaN NaN -1.6 82 0.426829268293 -21.40 -20.10 -18.70 #.((((((..((.((.(((.....(((((.(....(.(((((.(.##################################### 2,45 5,46 #####################.(((.(((.((((...((.((.....((.(((((.........((((((((. NA NA NA NA NA
Columns:
Column Number | Description |
---|---|
1 | Chromosome |
2 | Start (0-based) |
3 | End (1-based) |
4 | snoRNA ID |
5 | Chimera count |
6 | Strand |
7 | Interaction energy (PLEXY) |
8 | Interaction structure (PLEXY) |
9 | Interaction sequence (PLEXY) |
10 | Box |
11 | Modification position (1-based) |
12 | Interaction energy with random snoRNA (PLEXY) |
13 | snoRNA sequence length |
14 | GC fraction in snoRNA seuqnce |
15 | Interaction energy (RNAduplex) |
16 | Interaction energy with random snoRNA (RNAduplex) |
17 | Interaction energy with shuffled target sequence (RNAduplex) |
18 | Structure along snoRNA (RNAduplex) |
19 | snoRNA positions (RNAduplex) |
20 | Target positions (RNAduplex) |
21 | Genecode gene type eg. protein_coding |
22 | ENSEMBL ID |
23 | Gene name |
24 | Transcrip region eg. intron |
25 | mRNA region eg. five_prime_UTR |
RNAduplex is used as an alternative to PLEXY which is not bound to the specific snoRNA-target interaction. This part of the pipeline is used to generate a profile of bound/unbound positions along given snoRNA based on the column 18 (Structure along snoRNA) of the clustered RNAduplex results. One can view these plots as an aggregation of RNAduplex-calculated structures for each snoRNA-target chimeric pairs.