Help to interpret results of kisSplice
I am analysing the alternative splicing in my rna seq reads. NO reference genome is available. KIsSplice is adapted to this purpose.
I ran kissSplice on example data . I got the results folder containing many files. The user guide does not explain how to interpret the results, which is especially required for the naive non experts to this field. I got the the following files
type 1.fa
>bcc_1|Cycle_0|Type_1|upper_path_length_278|C1_0|C2_50|rank_1.00000
CGGACGCGCAAAATACAATAAAAAGGAAGGAAGAAAACGAAGTATCGCTATCTGCAAAGGCAGATCAAACTTGCTCGGCCAAATAAAAACACTTTGTAAATGAGTCTGAGCCACGCAGTTCGCTTGACAAGTTTTCCTCGGCTTGTCCAAAGAAAGTTGTAACAAATGTACATCAAATGAACAAGTTTTACCCAACACTTTCTCAGGCTAACAAATACTCTGCAGTTTCTGGCAGGGATACAGCGAGTGAGTGATCCCGCCATCATGAGCAAGAAGCC
>bcc_1|Cycle_0|Type_1|lower_path_length_82|C1_8|C2_0|rank_1.00000
CGGACGCGCAAAATACAATAAAAAGGAAGGAAGAAAACGAAATACAGCGAGTGAGTGATCCCGCCATCATGAGCAAGAAGCC
.edges file
0 1 RF
1 0 RF
1 2 RR
1 5 FR
2 3 RF
2 1 FF
3 2 RF
3 4 RR
4 5 RR
4 3 FF
5 1 FR
5 4 F
.nodes file
0 CAAAGAAAGTTGTAACAAATGTACATCAAATGAACAAGTTGTACCCAACACTTTCTCAGGCTAACAAATACTC
1 AACTTGTTCATTTGATGTACATTTGTTACAACTTTCTTTGGACAAGCCGAGGAAAACTTGTCAAGCGAACTGCGTGGCTCAGACTCATTTACAAAGTGTTTTTATTTGGCCGAGCAAGTTTGATCTGCCTTTGCAGATAGCGATACTTCGTTTTCTTCCTTCCTTTTTATTGTATTTTGCGCGTCC
2 GCTTCTTGCTCATGATGGCGGGATCACTCACTCGCTGTATCCCTGCCAGAAACTGCAGAGTATTTGTTAGCCTGAGAAAGTGTTGGGTAAAACTTGTTCATTTGATGTACATTTGTTACAACTTTCTTTG
3 ATACAGCGAGTGAGTGATCCCGCCATCATGAGCAAGAAGCCGACAGCCGGACCGGCGCTCCACAAGGTCATAATGGTGGGCAGTGGCGGCGTGGGAAAGTCCGCCCTCACACTGCAGTTTATGTACGATGAGTTCGTCGAGGACTACGAGCCCACCAAGGCCGATAGCTATAGGAAAAAGGTTGTGCTGGACGGCGAGGAAGTACAAATAGATATATTGGATACGGCTGGCCAGGAGGATTATGCCGCCATCAGAGATAACTACTTTCGCAGCGGCGAGGGTTTCCTTTGCGTCTTCTCCATCACAGACGACGAAAGCTTCCAGGCAACCCAGGAATTCAGAGAACAAATCTTGCGGGTGAAGAATGATGAGAGCATACCGTTCCTGCTGGTGGGCAACAAGTGCGATCTGAATGATAAGCGCAAGGTGCCGCTGAGCGAGTGCCAGCTGAGGGCGCAGCAGTGGGCGGTGCCCTATGTGGAGACCTCGGCTAAAACCCGCGAAAATGTGGACAAGGTATTTTTTGATTTGATGCGCGAAATAAGATCACGAAAAACCGAAGATTCGAAAGCCACGAGCGGGCGTGCTAAAGATAGATGCAAGAAGCGGAGACTTAAGTGTACCCTACTTTAGGCATTAGGTATTTTATGATCTAATCAGGGATATTTCATCGCGTAAAAAACAACGTCAGACGGACGTGAAACAGCCGCCGAAGCCCAACTCTCATTGCTGCCAACTGCTGTAGGATGATGAAGAACAACAACGGACAACAACCATACGATGAACAACAAAACAACTGCAGCAGCAACAAATTGGAAAATAACACAACGGCCACACGGATGATAACACCAACACACAGGATATGAAGGATATGGAGAACGGAACCATATGTTAATACAATTTAATTAATTAACTTTGAGAACACCAGTACACACATACGAACAGCAACAGATATTAAAACTATTTGCCACACTCAGAAACTCAAAATCCATAATCCACGTTAACTTTCATTGTAATATACATAAATATATATATATATATATATATGATTTAGGCAACAAGTTTTTTTTTCGAAAACATCAAGCGAAAAGCACACAGACGGGCAACTTACGAATTCTGTCGTTTATTTTTGGTTACTTATTTTTTTTTTTTTTTGAATCATCGATGTTTGTTTGTGTTGCCTCCGTAAAAAAAAAATGTTAAAACTAAAACCTAAAGCTGAAGCTAACGCTTAAACATATTAAATATAATCATCAATCGTAGACAACTAAAGAAGCCCATAATAATTATGCAATTTAAAACTTGCTACAGATATTTCTCTTGTTTAATTATATATACGCATACATTTTTTTGTAATATTTTTAAAGTTTAATAGCAAAATGCAAACCACACAAACCAACAAGAAACCACACAGAAAAGCTTTTTATAAATATATCTAAATATATATTTAAATATATATAAAATAGTATAAAACACTTAAAATCCTAGCGAAGAAACAACAGAGGAAAGCGGGGAGAAAGAAAAAACAGAAAAACAACAAATATCTCCAATTATTAATTGTAAACGAAGTGAATCGAAACAAATTTTTAATGCAATTTTTGTAATTTTCTAAACCGAAAGCAAATGTGTAGGGATTTATAAACAACAACAAAACCAATGAGTAATAATGGTACACACTAATGTTTCTGACAAGCTTTGGAGACTTTCCGTTACAAATAGTTATTTTCTTTGCCCTGGAACACATCCAATATATGTATATGTATGTATGTATGTATGTTTAGCAATTACTCCCGATTGATTTGCTTCTTTGTTTACTTTTGTATAACTGCATTCTGTATTGTAATATTTAAGCTATTATTATTATGATAATTATTATTATTATTAAATATATAAGTTATATATGCA
4 GGACGCGCAAAATACAATAAAAAGGAAGGAAGAAAACGAAATACAGCGAGTGAGTGATCCCGCCATCATGAGCAAGAAGC
5 CTTTCACACTAGTTTCTTTCAAGCAAGCAAAACCAACGGAACTTTAATTGCGGTGTGCGGCGAACGAGAAGAGAAACCGAAAAGCAGCCAATTTACTGTTGCGTTCCGATCCTGTTAATTCATCAGTTGCCGATTCTCCGATCGCGCCTGTAACTTTTTTGTTTAGTTTAGTGCATCAAGTGCGAGATAACACAGCAAAGCAACAACAAACGAAGCGACAGGCCAAAGCGGACGCGCAAAATACAATAAAAAGGAAGGAAGAAAACGAA
How can these results be interpreted? Is there any way way to graphically show these results.
thanks
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majeedaasim •
1 answer
Dear user, The introductory slides we use in our trainings should help you. You can find them here: http://kissplice.prabi.fr/training/ Best regards, Vincent
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