Kissplice: Problem getting SNPs in test data

Question

[WeepingMeadow]

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

Answer 1

[leandro.ishi.lima]

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.

Answer 2

[bilal.sarwar]

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.

[leandro.ishi.lima]

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.

Answer 3

[leandro.ishi.lima]

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.