Error in running kissplice2reftranscriptome

Question

[sandravelasco911012]

Dear all, I'm run into an error when running kissplice2reftranscriptome; the error was:

Opening all files and formatting tables...
Collecting data...
Traceback (most recent call last):
File "kissplice2reftranscriptome", line 577, in <module>
main()
File "kissplice2reftranscriptome", line 349, in main
codonTable), isSpecificCondition, pval, deltaf, componentSize)
TypeError: writeInMergedBubblesTsv() takes exactly 8 arguments (9 given)

I don't understand what is the problem, all my files looks good. My command line was:

kissplice2reftranscriptome -b Trinity.fasta.transdecoder.bed -k type0b.fa -t total.psl -s kissDE_results_table_filtered.tab

Thanks in advance for your help.

[1012254696]

Dear sir, I have the same problem with yours. Have you had solved it?

Answer 1

[bioinformatics2020]

usage: kissplice2reftranscriptome 
[-h -b PATH_TO_ORF_FILE ]
[-k PATH_TO_KISSPLICE_FILE 
[-t PATH_TO_BLAT_FILE
[-s PATH_TO_KissDE_FILE]
[-pval P_VALUE]
[-o PATH_TO_MAIN_OUTPUT_FILE]
[-l PATH_TO_LOW_QUERY_COVERAGE_OUTPUT_FILE]
[-m PATH_TO_MERGED_BUBBLES_OUTPUT_FILE]
[-u PATH_TO_UNTREATED_BUBBLES_OUTPUT_FILE]
[-Q QC_MIN] [-C KC_MIN] [-K K_VAL]
[--merge_codon]

Check to see if you're missing any of those, or if you're using the correct files.

Answer 2

[vincent.lacroix]

Dear user,

KisSplice outputs several files. To start, I would recommend using the file "type0a.fa" which correspond to simple SNPs. The file "type0b.fa" corresponds to multiple SNPs located less than k nt apart.

Best,

Vincent