Mercurial > repos > peterjc > blast_top_hit_species
changeset 1:8e86daf42b9c draft
Uploaded with disclaimer and known issues in README
author | peterjc |
---|---|
date | Mon, 30 Mar 2015 11:23:23 -0400 |
parents | 2e96bf82b463 |
children | b0e6dbc9041d |
files | README.rst |
diffstat | 1 files changed, 32 insertions(+), 0 deletions(-) [+] |
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--- a/README.rst Mon Mar 30 11:07:48 2015 -0400 +++ b/README.rst Mon Mar 30 11:23:23 2015 -0400 @@ -14,6 +14,7 @@ This is an example workflow using the Galaxy wrappers for NCBI BLAST+, see https://github.com/peterjc/galaxy_blast + Galaxy workflow for counting species of top BLAST hits ====================================================== @@ -83,6 +84,37 @@ Note the nematode count in this image was shown as a mouse-over effect. +Disclaimer +========== + +Species assignment by top BLAST hit is not suitable for any in depth +analysis. It is particularly prone to false positives where contaiminants +in public datasets are mislabled. See for example Ed Yong (2015), +"There's No Plague on the NYC Subway. No Platypuses Either.": + +http://phenomena.nationalgeographic.com/2015/02/10/theres-no-plague-on-the-nyc-subway-no-platypuses-either/ + + +Known Issues +============ + +This workflow uses the Galaxy "Count" tool, version 1.0.0, as shipped with +the current stable release (Galaxy v15.03, i.e. March 2015). + +The updated "Count" tool version 1.0.1 includes a fix not to remove spaces +in the fields being counted. In the example above, while the top hits are +not affected, minor entries like "cellular slime molds" are shown as +"cellularslimemolds" instead (look closely at the Pie Chart key).. + +The updated "Count" tool version 1.0.1 also adds a new option to sort the +output, which avoids the additional sorting step in the current version of +the workflow. + +A future update to this workflow will use the revised "Count" tool, once +this is included in the next stable Galaxy release - or migrated to the +Galaxy Tool Shed. + + Availability ============