Question: Kissplice: Problem getting SNPs in test data
0
gravatar for WeepingMeadow
29 days 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 • 112 views
ADD COMMENTlink modified 29 days ago by leandro.ishi.lima70 • written 29 days ago by WeepingMeadow0
1
gravatar for leandro.ishi.lima
29 days 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 29 days ago by leandro.ishi.lima70
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