Question: Help to interpret results of kisSplice
0
gravatar for majeedaasim
4 weeks ago by
majeedaasim20
United States
majeedaasim20 wrote:

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

ADD COMMENTlink modified 2 days ago by vincent.lacroix50 • written 4 weeks ago by majeedaasim20

Please use sensible tags for your question(s). At the very minimum, you should have added "kissplice". This enables developers to easily find questions about their tools. I have added this tag to your question now.

I also added markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

101010 Button

ADD REPLYlink written 4 weeks ago by WouterDeCoster22k
1
gravatar for vincent.lacroix
2 days ago by
vincent.lacroix50 wrote:

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

ADD COMMENTlink written 2 days ago by vincent.lacroix50
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