Easy comparison between Whippet, SplAdder and DExSeq differential splicing analyses
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11 weeks ago
graeme.thorn ▴ 60

I have run SplAdder, Whippet and DExSeq on some RNA-seq data from 67 tissues, grouped into multiple groups. I was quickly wondering if there was an easy way of comparing the differential splicing events called between groups called by the different tools?

EDIT (to clarify): I have a list of events in SplAdder's output format

event_id    gene    p_val   p_val_adj   mean_event_count_A  mean_event_count_B  log2FC_event_count  mean_gene_exp_A mean_gene_exp_B log2FC_gene_exp
alt_3prime_256756   ENSG00000157426 1.92533988752075e-10    1.35366073407139e-05    1.37149613922869    5.8684525830872 -2.09722957692087   8550.13829278468    7073.77244726469    0.273467944385139
alt_3prime_121744   ENSG00000103544 3.02244118621786e-10    1.35366073407139e-05    1.16161885542651    6.34426946402131    -2.44931727230988   21392.9702073256    14807.2384446179    0.530834198122625
...

and events in Whippet's output format:

Gene    Node    Coord   Strand  Type    Psi_A   Psi_B   DeltaPsi    Probability Complexity  Entropy
ENSG00000226919 15  chr1:240775805-240776044    +   TE  0.13789 0.86466 -0.72676    1   K3  0
ENSG00000226919 16  chr1:240776045-240776222    +   TE  0.86619 0.12764 0.73856 1   K3  0
...

and events in DExSeq format:

groupID featureID   exonBaseMean    dispersion  stat    pvalue  padj    genomicData.seqnames    genomicData.start   genomicData.end genomicData.width   genomicData.strand  countData.1_B   countData.2_A   countData.3_A   countData.4_A   countData.5_A   countData.6_RM  countData.7_A   countData.8_A   countData.9_A   countData.10_A  countData.11_A  countData.12_A  countData.13_A  countData.14_A  countData.15_A  countData.16_B  countData.17_A  countData.18_A  countData.19_A  countData.20_B  countData.21_A  countData.22_A  countData.23_A  transcripts
ENSG00000006194+ENSG00000281005 E012    120.36738231679 0.0153240977271502  19.489210901958 1.01169503974414e-05    0.0256654971642218  chr16   3285059 3285239 181 +   85  136 166 81  79  65  216 51  152 133 116 75  165 174 174 90  94  71  118 122 222 149 165 ENST00000219069
ENSG00000006282+ENSG00000049283 E028    41.1223020123828    0.0485295754805495  14.6249162606412    0.00013116880397402 0.0889322169372101  chr17   50536710    50536726    17  +   39  4   38  16  34  27  90  5   52  32  19  6   185 29  73  49  28  28  37  32  38  58  100 c("ENST00000574464", "ENST00000507467", "ENST00000507998", "ENST00000511414", "ENST00000507709", "ENST00000512291", "ENST00000268933", "ENST00000512379", "ENST00000537145", "ENST00000510045", "ENST00000515126", "ENST00000503246")

and I would like to see if the same events are appearing in the three different tools (I am aware that DExSeq gives results in terms of 'exons' or segments of exon, so that might need a bit more fiddling to compare directly)

SplAdder DExSeq splicing Whippet • 257 views
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