diff --git a/notebooks/AnoPrimer-short.ipynb b/notebooks/AnoPrimer-short.ipynb index 6ee5ab8..1e55bfe 100644 --- a/notebooks/AnoPrimer-short.ipynb +++ b/notebooks/AnoPrimer-short.ipynb @@ -52,7 +52,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": null, "metadata": { "id": "NCEovYA6RrH4", "cellView": "form" @@ -64,7 +64,7 @@ "\n", "species = 'gambiae_sl' #@param [\"gambiae_sl\", \"funestus\"]\n", "assay_type = 'cDNA primers' #@param [\"gDNA primers\", \"gDNA primers + probe\", \"probe\", \"cDNA primers\"]\n", - "assay_name = 'coeae2f' #@param {type:\"string\"}\n", + "assay_name = 'Cyp6p3' #@param {type:\"string\"}\n", "min_amplicon_size = 60 #@param {type:\"integer\"}\n", "max_amplicon_size = 120 #@param {type:\"integer\"}\n", "amplicon_size_range = [[min_amplicon_size, max_amplicon_size]]\n", @@ -74,7 +74,7 @@ "#@markdown\n", "#@markdown primer_target should be a region string ('2L:28545767') for gDNA primers and probes, and an AGAP transcript identifier for cDNA primers.\n", "\n", - "primer_target = 'AGAP006228-RA' #@param {type:\"string\"}" + "primer_target = 'AGAP002865-RA' #@param {type:\"string\"}" ] }, { @@ -122,7 +122,7 @@ { "cell_type": "markdown", "source": [ - "Finally, lets evaluate our primers, by looking for SNPs in the primer binding sites, plotting the primer locations in contrast to any nearby genes and exons, and in the case of *An. gambiae s.l*, checking for specificity by aligning to the *An. gambiae* genome. You may want to change the Ag1000g sample set that we compare to. To see a full list of available sample sets, you can run `primers.summarise_metadata()`" + "Finally, lets evaluate our primers, by looking for SNPs in the primer binding sites, plotting the primer locations in contrast to any nearby genes and exons, and in the case of *An. gambiae s.l*, checking for specificity by aligning to the *An. gambiae* genome." ], "metadata": { "id": "4Sq8x55m-sDI" @@ -136,7 +136,7 @@ }, "outputs": [], "source": [ - "primers.evaluate_primers(sample_sets=['AG1000G-BF-A'], sample_query=None, out_dir=\"./\")" + "primers.evaluate_primers(sample_sets='3.0', sample_query=None, out_dir=\"./\")" ] } ],