number of loci in the catalog created by ustacks (polymorphic and not polymorphic)

[Li]

Dear Julian and stacks users

I wish to find the number of loci in the catalog created by ustacks, I used de novo map commend, and I cant find this number.

To my understanding the file  XXX.tags.tsv: assembled loci, should have all loci regardless to their polymorphism, unfortunately in the file I get this is not the case, and the number of loci there is the same number as I get before filtering in the population program.  

If I can find this number somewhere in the log file of the denovo_map please tell me where is it in the file, under what definition? because I have not found.

I'll appreciate your help

Thanks

Li

[Nicolas Rochette]

Hi Li,

"batch_X.catalog.tags.tsv" contains the list of the loci in the catalog, and "batch_X.catalog.snps.tsv" contains the polymorphisms known by the catalog (see the online manual, http://catchenlab.life.illinois.edu/stacks/manual/). But maybe that is not the question ?

Best,

Nicolas

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[Li]

Thank you for the answer,

 

But if this is true then something in my analysis is very wrong because:

In the "batch_X.catalog.tags.tsv" I see 104150 loci (as I understand this is all loci in the catalog regardless to their polymorphism)

in the "batch_X.catalog.snps.tsv" I see 83089 snps spread in 36997 loci, and this means that about 35% of the loci that was discovered in denovo_map are polymorphic. This can't be right isn't it?

 

I perform a ddRAD sequencing on populations of one non model spices.

Thanks 

Li 

[Nicolas Rochette]

Hi Li,

Having 60% of monomorphic loci is not necessarily abnormal, depending on the length of the reads and the nucleotide diversity in your system. Still, you will want to check the average coverage in your data, as a low coverage may bias this number upwards.

Best,

Nicolas

[Alex Krohn]

Hi Nicholas,

Is there an easy way to check per locus or average individual coverage in Stacks? I can't seem to find any information about this very basic procedure....

-Alex

[Julian Catchen]

The basic procedure of reporting average depth of coverage is handled by
both pstacks and ustacks which will output the depth of coverage for the
sample processed. If you are running denovo_map.pl or ref_map.pl these
coverages are aggregated into a table and the table of coverages is
output to the terminal and recorded in the log file.

Per-individual, per-locus depth of coverage is reported in the web
interface, or with export_sql.pl, or on a SNP-by-SNP basis in the VCF
file, or in the *.matches.tsv files.

julian

Alex Krohn wrote:
> Hi Nicholas,
>
> Is there an easy way to check per locus or average individual coverage
> in Stacks? I can't seem to find any information about this very basic
> procedure....
>
> -Alex
>
> On Thursday, August 4, 2016 at 3:58:33 PM UTC-7, Nicolas Rochette wrote:
>
> Hi Li,
>
> Having 60% of monomorphic loci is not necessarily abnormal,
> depending on the length of the reads and the nucleotide diversity in
> your system. Still, you will want to check the average coverage in
> your data, as a low coverage may bias this number upwards.
>
> Best,
>
> Nicolas
>
> Li wrote on 07/01/2016 02:58 PM:
>>
>> Thank you for the answer,
>>
>> But if this is true then something in my analysis is very
>> wrong because:
>>

>> In the "batch_X.catalog.tags.tsv" I see *104150* loci (as I

>> understand this is all loci in the catalog regardless to their
>> polymorphism)
>>
>> in the "batch_X.catalog.snps.tsv" I see 83089 snps spread in

>> *36997* loci, and this means that about 35% of the loci that
>> was discoveredin denovo_map are polymorphic. This can't be

>> right isn't it?
>>
>> I perform a ddRAD sequencing on populations of one non model
>> spices.
>>
>>
>> Thanks
>> Li
>> --
>> Stacks website: http://catchenlab.life.illinois.edu/stacks/
>> <http://catchenlab.life.illinois.edu/stacks/>
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>
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--
Julian Catchen, Ph.D.
Assistant Professor
Department of Animal Biology
University of Illinois, Urbana-Champaign
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jcat...@illinois.edu; @jcatchen