Commit 1a75eaba authored by Romain Feron's avatar Romain Feron
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Quick README update - fixes

parent 79bf1bc2
......@@ -43,12 +43,11 @@ Before running the pipeline, you should prepare the following elements:
raw sequencing reads can be demultiplexed using [Stacks](http://catchenlab.life.illinois.edu/stacks/comp/process_radtags.php)
or [pyRAD](http://nbviewer.jupyter.org/gist/dereneaton/af9548ea0e94bff99aa0/pyRAD_v.3.0.ipynb#The-seven-steps-described).
- A **population map** (popmap): a tabulated file with individual ID as the first column and sex as the second column.
It is important that the individual IDs in the popmap are the same as the names of the demultiplexed reads files (see the [popmap section](#population-map) for details).
It is important that the individual IDs in the popmap are the same as the names of the demultiplexed reads files (see the doc for details).
- If you want to map the sequences to a reference genome: a **reference genome** in fasta format.
Note that when visualizing `mapping` results with `radsex-vis`, linkage groups / chromosomes are automatically inferred from scaffold names in the reference sequence
if their name starts with *LG*, *chr*, or *chromosome* (case unsensitive).
If chromosomes are named differently in the reference genome, you should prepare a tabulated file with
reference scaffold ID in the first column and corresponding chromosome name in the second column (see the [chromosomes names section](#chromosomes-names) for details)
If chromosomes are named differently in the reference genome, you should prepare a tabulated file with reference scaffold ID in the first column and corresponding chromosome name in the second column (see the doc for details)
#### Computing the coverage table
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