Question: Kissplice: Problem getting SNPs in test data
0
gravatar for WeepingMeadow
3 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 • 146 views
ADD COMMENTlink modified 3 months ago by leandro.ishi.lima70 • written 3 months ago by WeepingMeadow0
1
gravatar for leandro.ishi.lima
3 months ago by
leandro.ishi.lima70 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 3 months ago by leandro.ishi.lima70
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