Open angelaparodymerino opened 5 years ago
Yes, right. That is only a default setting for general situation. You could change it based on your own situation.
Yibo
On Wed, Jul 10, 2019, 5:09 PM Angela Parody-Merino notifications@github.com wrote:
Hi,
I am a molecular biologist. Briefly, I am working on a non-model species, with no genomic data. I have some Genotyping-By-Sequencing data from different populations and I want to use npGeno to obtain variants (SNPs) between those populations.
Anyway, I am wondering why the Getting started with npGeno.pdf asks you to set a k-mer length to 100 (for Minia). According to what I read (i.e. https://github.com/rrwick/Bandage/wiki/Effect-of-kmer-size http://url the "optimal" k-mer length depends on the length of your reads, the depth of coverage of the reads and the genome size. Since I don't have genome size information (although it is estimated to be 1.4Gb), I have also found in biostars forums that a good k-mer size to choose would be 2/3 of the reads size. In my case, reads are mostly 90-95bp, therefore I think I should choose a k-mer of ~61. Am I right?
Thanks in advance,
'Angela Parody Merino
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Hi Yibo, thanks for your quick answer. Maybe it is a stupid question, but how could I change it?
Thanks in advance,
'Angela Parody Merino
You have to read Perl script and revise script arguments. If you can not, you have to use default settings. Yibo
On Wed, Jul 10, 2019, 11:08 PM Angela Parody-Merino < notifications@github.com> wrote:
Hi Yibo, thanks for your quick answer. Maybe it is a stupid question, but how could I change it?
Thanks in advance,
'Angela Parody Merino
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Ok, I see. Last question, I am not completely sure: What do you mean by set (in the .csv file)? is each of the samples one set?
Thanks in advance,
'Angela
Yes
On Wed, Jul 10, 2019, 11:27 PM Angela Parody-Merino < notifications@github.com> wrote:
Ok, I see. Last question, I am not completely sure: What do you mean by set (in the .csv file)? is each of the samples one set?
Thanks in advance,
'Angela
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Hi,
I am a molecular biologist. Briefly, I am working on a non-model species, with no genomic data. I have some Genotyping-By-Sequencing data from different populations and I want to use npGeno to obtain variants (SNPs) between those populations.
Anyway, I am wondering why the Getting started with npGeno.pdf asks you to set a k-mer length to 100 (for Minia). According to what I read (i.e. https://github.com/rrwick/Bandage/wiki/Effect-of-kmer-size the "optimal" k-mer length depends on the length of your reads, the depth of coverage of the reads and the genome size. Since I don't have genome size information (although it is estimated to be 1.4Gb), I have also found in biostars forums that a good k-mer size to choose would be 2/3 of the reads size. In my case, reads are mostly 90-95bp, therefore I think I should choose a k-mer of ~61. Am I right?
Thanks in advance,
'Angela Parody Merino