denovo_map.pl

[Dongmin Kim]

Hi, 

I finished process_radtags and clone filter. It's time to do denovo.map.pl. But I have no idea how it works even though I read the manual.. 

Also, Do I need to do this on mysql server? or same as process_radtags (just on bash?)

First of all, we don't have a reference so we are using denovo_map .pl and don't use a population map. 

From the document my professor provided, it says to use this command, 

denovo_map.pl -T 10 -o ./stacks2 -B Ambystoma_radtags -b 1 -D "Waye 3 pool (X2) analysis" --samples Ambystoma_RADseq_filtered_Oct2016/ -O ./stacks2/popmap.txt

(What are the "-B", "-b", "-D", and "-O"??)  I know -o is path to write pipeline output files, -T is the number of threads/CPUs to use (not quite understand this part)

But when I look at the manual, it only says this,

denovo_map.pl --samples dir --popmap path -o dir [--paired] (assembly options) [-X prog:"opts" ...]

Input/Output files:

• --samples [path] — specify a path to the directory of samples (samples will be read from population map).
• --popmap [path] — path to a population map file (format is "[name] TAB [pop]", one sample per line).
• o [path] — path to write pipeline output files.

General options:

• X — additional options for specific pipeline components, e.g. -X "populations: -p 3 -r 0.50".
• T — the number of threads/CPUs to use (default: 1).
• d — Dry run. Do not actually execute anything, just print the commands that would be executed.

Stack assembly options:

• M — number of mismatches allowed between stacks within individuals (for ustacks).
• n — number of mismatches allowed between stacks between individuals (for cstacks).
• --gapped — perform gapped comparisons (for ustacks, cstacks, sstacks; default: off).

SNP model options:

• --var-alpha — significance level at which to call variant sites (for gstacks; default: 0.05).
• --gt-alpha — significance level at which to call genotypes (for gstacks; default: 0.05).

Paired-end options:

• --paired — after assembling RAD loci, assemble contigs for each locus from paired-end reads.

Miscellaneous:

• --time-components — (for benchmarking)

Thanks 

[Nicolas Rochette]

Please have a look at the manual for version 1 (http://catchenlab.life.illinois.edu/stacks/manual-v1/) and version 2 (http://catchenlab.life.illinois.edu/stacks/manual/)

Best,

Nicolas

--
Stacks website: http://catchenlab.life.illinois.edu/stacks/
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