From 4b305090b4df90844b6db90eda76d533ae4c24d5 Mon Sep 17 00:00:00 2001 From: Nick Moore Date: Sat, 13 Apr 2024 08:53:40 +1000 Subject: [PATCH] fixes --- docs/getting-started/index.md | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/docs/getting-started/index.md b/docs/getting-started/index.md index 7036965..984ef7a 100644 --- a/docs/getting-started/index.md +++ b/docs/getting-started/index.md @@ -109,14 +109,14 @@ In this case, we're expanding the column `count` into two new columns, ### 4. Calculating Scores Now we have pivoted the data, for each sequence we have counts at -two different time points. We want calculate scores from the counts. -one by the other: +two different time points. We want to calculate scores from the counts +by dividing one by the other: [![Example 1 Image 4](img/example_1_4.png)](img/example_1_4.png) The [Python Code](../included-plugins/#python) tool lets us write small expressions in Python and apply them to each row of the table. In this case we're calculating -score as the fraction of sequences which have survived from time 1 +a simplified score as the fraction of sequences which have survived from time 1 to time 2. ### 5. Saving Results @@ -166,6 +166,11 @@ TGTAGTGCCGTATTTGTGGC,ATGCTTTGTACGGGTGGTGCCCTGGCTTATCTATCTAGATCCGTCTCCGAGTCACGGTC ``` *(etc)* +The first three barcode map to the same sequence, +the other two have SNVs but they are hard to spot! +There are 1000 barcodes in the file, about 1/4 of which +map to unmodified sequences. + First, we modify our sequence reading and grouping steps to rename the sequence column to `barcode`, for clarity.