Question: k2rt couldn't deal with type3(indel) fasta?
gravatar for ku1.heyi.92f
9 months ago by
ku1.heyi.92f0 wrote:


By k2rt, I'm now trying to detect short indels (Not SNPs) which cause non-synonymous amino acid substitutions. I already get input files:

kissplice result (XXX_coherent_type_3.fa) kissDE result blat result file bed result file

But when I try to run k2rt, Type error occurs.

error message is :

Opening all files and formatting tables... Collecting data...

File ".../.pyenv/versions/2.7.10/bin/kissplice2reftranscriptome", line 4, in <module> __import__('pkg_resources').run_script('kissplice2reftranscriptomelib==1.3.2', 'kissplice2reftranscriptome') File ".../.pyenv/versions/2.7.10/lib/python2.7/site-packages/pkg_resources/", line 729, in run_script self.require(requires)[0].run_script(script_name, ns) File ".../.pyenv/versions/2.7.10/lib/python2.7/site-packages/pkg_resources/", line 1649, in run_script exec(script_code, namespace, namespace) File ".../.pyenv/versions/2.7.10/lib/python2.7/site-packages/kissplice2reftranscriptomelib-1.3.2-py2.7.egg/EGG-INFO/scripts/kissplice2reftranscriptome", line 577, in <module>

File ".../.pyenv/versions/2.7.10/lib/python2.7/site-packages/kissplice2reftranscriptomelib-1.3.2-py2.7.egg/EGG-INFO/scripts/kissplice2reftranscriptome", line 356, in main

TypeError: writeInMergedBubblesTsv() takes exactly 8 arguments (9 given)

I'd like to know whether indel analysis is possible by k2rt.

ADD COMMENTlink modified 9 months ago by vincent.lacroix80 • written 9 months ago by ku1.heyi.92f0
gravatar for vincent.lacroix
9 months ago by
vincent.lacroix80 wrote:

Dear User,

Unfortunately, k2rt does not support indels for now. This is something we are interested in developing, but we have nothing ready.

Best regards,


ADD COMMENTlink written 9 months ago by vincent.lacroix80

Thank you very much. I'm looking forward to new k2rt.


ADD REPLYlink written 9 months ago by ku1.heyi.92f0
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