KisSplice2RefTranscriptome does not preserve cycle

Question

[pauloneill27]

* My dumb mistake - I forgot to rerun the BLAT step again for my new set of results. *

Hello I am running KisSplice2RefTranscriptome on the output of kissplice and a transcriptome generated by trinity. It seems to work well except that that the Cycle number in the Bubble seems to be reset to zero by KisSplice2RefTranscriptome.

This means that I cannot simply map the ks2rt data to the kissplice data. In the example below, Cycle_3 from kissplice has become Cycle_0 in ks2rt

I am using version 1.3.2

any advice on this?

thanks

Paul

dok41_coherents_type_0a.fa:>bcc_10005|Cycle_3|Type_0a|upper_path_length_83|C1_1|C2_1|C3_2|C4_2|C5_1|C6_0|C7_0|C8_0|C9_2|C10_2|C11_0|C12_0|Q1_67|Q2_66|Q3_68|Q4_68|Q5_60|Q6_0|Q7_0|Q8_0|Q9_68|Q10_60|Q11_0|Q12_0|rank_0.84686 dok41_coherents_type_0a.fa:>bcc_10005|Cycle_3|Type_0a|lower_path_length_83|C1_0|C2_0|C3_1|C4_0|C5_0|C6_0|C7_1|C8_0|C9_0|C10_0|C11_0|C12_1|Q1_0|Q2_0|Q3_71|Q4_0|Q5_0|Q6_0|Q7_71|Q8_0|Q9_0|Q10_0|Q11_0|Q12_72|rank_0.84686

mainOutput.tsv:TRINITY_DN463_c0_g1_i12 bcc_10005|Cycle_0|Type_0a True 100.0 546 TCT CCT S P TrueTrue True False 100.0|100.0|66.67|100.0|100.0|0.0|0.0|0.0|100.0|100.0|0.0|0.0 C1_1|C2_1|C3_2|C4_2|C5_1|C6_0|C7_0|C8_0|C9_2|C10_2|C11_0|C12_0 C1_0|C2_0|C3_1|C4_0|C5_0|C6_0|C7_1|C8_0|C9_0|C10_0|C11_0|C12_1 N/A N/A N/A mainOutput.tsv:TRINITY_DN463_c0_g1_i7 bcc_10005|Cycle_0|Type_0a True 100.0 3123 TCT CCT S P TrueTrue True False 100.0|100.0|66.67|100.0|100.0|0.0|0.0|0.0|100.0|100.0|0.0|0.0 C1_1|C2_1|C3_2|C4_2|C5_1|C6_0|C7_0|C8_0|C9_2|C10_2|C11_0|C12_0 C1_0|C2_0|C3_1|C4_0|C5_0|C6_0|C7_1|C8_0|C9_0|C10_0|C11_0|C12_1 N/A N/A N/A mainOutput.tsv:TRINITY_DN463_c0_g1_i14 bcc_10005|Cycle_0|Type_0a True 100.0 3079 TCT CCT S P TrueTrue True False 100.0|100.0|66.67|100.0|100.0|0.0|0.0|0.0|100.0|100.0|0.0|0.0 C1_1|C2_1|C3_2|C4_2|C5_1|C6_0|C7_0|C8_0|C9_2|C10_2|C11_0|C12_0 C1_0|C2_0|C3_1|C4_0|C5_0|C6_0|C7_1|C8_0|C9_0|C10_0|C11_0|C12_1 N/A N/A N/A mainOutput.tsv:TRINITY_DN463_c0_g1_i9 bcc_10005|Cycle_0|Type_0a True 100.0 2929 TCT CCT S P TrueTrue True False 100.0|100.0|66.67|100.0|100.0|0.0|0.0|0.0|100.0|100.0|0.0|0.0 C1_1|C2_1|C3_2|C4_2|C5_1|C6_0|C7_0|C8_0|C9_2|C10_2|C11_0|C12_0 C1_0|C2_0|C3_1|C4_0|C5_0|C6_0|C7_1|C8_0|C9_0|C10_0|C11_0|C12_1 N/A N/A N/A mainOutput.tsv:TRINITY_DN463_c0_g1_i3 bcc_10005|Cycle_0|Type_0a True 100.0 2512 TCT CCT S P TrueTrue True False 100.0|100.0|66.67|100.0|100.0|0.0|0.0|0.0|100.0|100.0|0.0|0.0 C1_1|C2_1|C3_2|C4_2|C5_1|C6_0|C7_0|C8_0|C9_2|C10_2|C11_0|C12_0 C1_0|C2_0|C3_1|C4_0|C5_0|C6_0|C7_1|C8_0|C9_0|C10_0|C11_0|C12_1 N/A N/A N/A mainOutput.tsv:TRINITY_DN463_c0_g1_i11 bcc_10005|Cycle_0|Type_0a True 100.0 2503 TCT CCT S P TrueTrue True False 100.0|100.0|66.67|100.0|100.0|0.0|0.0|0.0|100.0|100.0|0.0|0.0 C1_1|C2_1|C3_2|C4_2|C5_1|C6_0|C7_0|C8_0|C9_2|C10_2|C11_0|C12_0 C1_0|C2_0|C3_1|C4_0|C5_0|C6_0|C7_1|C8_0|C9_0|C10_0|C11_0|C12_1 N/A N/A N/A

Answer 1

[leandro.ishi.lima]

Dear pauloneill27,

Just to confirm, there are no problems here then?

Thanks for the report.

Kind regards.

Answer 2

[pauloneill27]

No there is no problem thanks for getting back. I could not delete the post. I have some promising results - kissplice is proving very useful thanks

Answer 3

[leandro.ishi.lima]

Dear pauloneill27,

Thanks for the confirmation! Please don't hesitate on contacting us in case of any doubt!

Kind regards.