gmap psl parsing in kissplice2refgenome

Question

[fabrice.legeai]

Hi,

I am trying to run kissplice2refgenome on a result of gmap in psl format of all type1 path found by kissplice. My psl file looks like that :

94 4 0 0 0 0 1 1 + bcc_99896|Cycle_0|Type_1|upper_path_length_98|C1_0|C2_0|C3_0|C4_0|C5_0|C6_0|C7_0| C8_0|C9_0|C10_0|C11_0|C12_0|C13_1|C14_1|C15_1|C16_0|C17_0|C18_0|C19_1|C20_1|C21_0|C22_0|C23_0|C24_1|rank_1.00000 98 0 98 GL3496981978137 194023 194122 2 39,59, 0,39, 194023,194063, 62 3 0 0 1 3 1 20 + bcc_99896|Cycle_0|Type_1|lower_path_length_82|C1_1|C2_3|C3_1|C4_1|C5_0|C6_0|C7_0| C8_0|C9_2|C10_0|C11_1|C12_1|C13_0|C14_0|C15_0|C16_0|C17_0|C18_0|C19_0|C20_0|C21_0|C22_0|C23_0|C24_0|rank_1.00000 82 14 82 GL3496242478080 758104 758189 2 26,39, 14,43, 758104,758150, 77 0 0 0 1 7 0 0 + bcc_99881|Cycle_2|Type_1|upper_path_length_84|C1_0|C2_0|C3_0|C4_0|C5_0|C6_0|C7_0| C8_0|C9_0|C10_0|C11_0|C12_0|C13_0|C14_0|C15_0|C16_1|C17_2|C18_2|C19_1|C20_1|C21_0|C22_1|C23_0|C24_1|rank_1.00000 84 0 84 GL349719744717 328931 329008 2 36,41, 0,43, 328931,328967, 77 0 0 0 0 0 0 0 + bcc_99881|Cycle_2|Type_1|lower_path_length_77|C1_1|C2_0|C3_0|C4_0|C5_0|C6_0|C7_0| C8_0|C9_0|C10_0|C11_2|C12_4|C13_0|C14_0|C15_0|C16_0|C17_0|C18_0|C19_0|C20_0|C21_0|C22_0|C23_0|C24_0|rank_1.00000 77 0 77 GL349719744717 328931 329008 1 77, 0, 328931, 80 0 0 0 1 25 0 0 - bcc_99817|Cycle_0|Type_1|upper_path_length_105|C1_0|C2_0|C3_0|C4_0|C5_0|C6_0|C7_0 |C8_0|C9_0|C10_0|C11_0|C12_0|C13_0|C14_0|C15_4|C16_5|C17_0|C18_0|C19_0|C20_0|C21_0|C22_0|C23_0|C24_0|rank_1.00000 105 0 105 GL350228299843 165859 165939 2 41,39, 0,66, 165859,165900, ...

And my command line like that : kissplice2refgenome gmap.psl -a ncbi_annotation_v2.gff3 -o kiss2genome.res --pairedEnd True

But I got the following error :

Traceback (most recent call last): File "/home/genouest/inrarennes/flegeai/local/kissplice/kissplice2refgenome-1.0.0/kissplice2refgenome", line 140, in <module> main() File "/home/genouest/inrarennes/flegeai/local/kissplice/kissplice2refgenome-1.0.0/kissplice2refgenome", line 119, in main previous_bcc_cycle, kissEventsmapped, boolEvent, beginningFile = event.getInfoFile(element,bloclist,previous_bcc_cycle,kissEventsmapped,fileW,int(opt ions.threshold),options.MAPPINGOUTPUT,options.countOption, options.pairedEnd, options.order,options.exonicReads,eventsToOutput,beginningFile, options.readLength, options.overlap) TypeError: getInfoFile() takes exactly 18 arguments (16 given)

Would you please help ?

Thanks a lot ! Fabrice

Answer 1

[vincent.lacroix]

Dear Fabrice, In principle, kissplice2refgenome takes both .psl and .sam as input. But in practice, we mostly use .sam files produced by STAR, using .gtf files dowloaded from Ensembl.

A typical workflow is given here: http://kissplice.prabi.fr/pipeline_ks_farline/

Overall we recommand to use STAR for mapping the bubbles to the reference genome, because it performs a bit better than gmap, which is more tailored towards mapping full-length transcripts. In our case, we do not assemble full-length transcripts. We only output the variables regions. When the sequences are short (which is the case for the lower paths of our bubbles), then the mapping positions reported by gmap are not always correct. This is the reason why we are slowly abandoning the .psl support in kissplice2refgenome.

However, iif you really want to use Gmap, please send us a sample file, and we can have a look at why it causes a bug in k2rg.

Cheers,

Vincent