Question: Kissplice: Problem getting SNPs in test data
0
gravatar for WeepingMeadow
6 months ago by
WeepingMeadow0 wrote:

Hello,

I looked at the forum but I couldn't find any answer to my question.

Since I don't have access to my actual dataset right now, I installed and tried test data to look for SNPs however results_reads1_reads2_k41_coherents_type_0a.fa or results_reads1_reads2_k41_coherents_type_0b.fa files are empty, It only gives output for Alternative Splicing events which is stored in results_reads1_reads2_k41_coherents_type_1.fa.

I used -s switch with either 1 or 2 but it still does not give me any results for SNP. Since I am new to SNP calling, I'm sorry if I'm asking something silly.

Thanks in advance! WM

kissplice snp • 280 views
ADD COMMENTlink modified 12 weeks ago by leandro.ishi.lima80 • written 6 months ago by WeepingMeadow0
2
gravatar for leandro.ishi.lima
6 months ago by
leandro.ishi.lima80 wrote:

Dear WeepingMeadow,

Unfortunately our test dataset only includes one alternative splicing event, which is found in file results_reads1_reads2_k41_coherents_type_1.fa. No SNPs are present, thus files results_reads1_reads2_k41_coherents_type_0a.fa and results_reads1_reads2_k41_coherents_type_0b.fa are indeed empty.

If you want to find SNPs in your real dataset, you have to use the -s switch (possibly coupled with the --experimental option, if you are facing long runtimes). If you have problems on doing so, please do not hesitate on recontacting us for further troubleshooting!

Kind regards.

ADD COMMENTlink written 6 months ago by leandro.ishi.lima80
0
gravatar for bilal.sarwar
12 weeks ago by
Pakistan/Lahore/CEMB-PU
bilal.sarwar0 wrote:

hello leandro

I am facing long runtime to prepare the KisSplice output file for KisSplice2rwfTranscriptome run. I used -s=1 switch too. please guide me how to solve this issue?

you wrote in your above answer (possibly coupled with the --experimental option, if you are facing long runtimes). ??????????????

I am sorry, I am new in Linux environment.

ADD COMMENTlink written 12 weeks ago by bilal.sarwar0

Dear Bilal Sarwar,

If KisSplice is taking too much time to run, you could try running the experimental algorithm by adding --experimental to your command line. It can be faster, at the cost of using more RAM.

Note also that by using -s 1 you will get only the Type0a-SNPs, which are single SNP within the sequence. If you are interested in multiple SNPs, you need to use -s 2.

You can find the full documentation of KisSplice options here: KisSplice Documentation

Kind regards.

ADD REPLYlink modified 12 weeks ago • written 12 weeks ago by leandro.ishi.lima80
0
gravatar for leandro.ishi.lima
12 weeks ago by
leandro.ishi.lima80 wrote:

Dear Bilal Sarwar,

If KisSplice is taking too much time to run, you could try running the experimental algorithm by adding --experimental to your command line. It can be faster, at the cost of using more RAM.

Note also that by using -s 1 you will get only the Type0a-SNPs, which are single SNP within the sequence. If you are interested in multiple SNPs, you need to use -s 2.

You can find the full documentation of KisSplice options here: KisSplice Documentation

Kind regards.

ADD COMMENTlink written 12 weeks ago by leandro.ishi.lima80
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