From 3ae22738656d148731f54001fa5c6c23d3f7f3fb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jonas=20S=C3=B6derberg?= Date: Fri, 23 Aug 2024 00:38:12 +0200 Subject: [PATCH] Update manipulating_vcf.md --- docs/Case_studies/manipulating_vcf.md | 17 ++++++++++++----- 1 file changed, 12 insertions(+), 5 deletions(-) diff --git a/docs/Case_studies/manipulating_vcf.md b/docs/Case_studies/manipulating_vcf.md index 0c1f758..f07380d 100644 --- a/docs/Case_studies/manipulating_vcf.md +++ b/docs/Case_studies/manipulating_vcf.md @@ -35,7 +35,7 @@ Finally, full gene names and functions found in this [file](https://ftp.flybase. #### Chromosome 4 -??? "_Hint, what do we need?_" +??? "_Hint_ **What do we need?**" Extract chr4 from the vcf and the gff and make new files ??? "_Hint_" @@ -50,10 +50,10 @@ Finally, full gene names and functions found in this [file](https://ftp.flybase. #### Making awking the data easier Start by splitting the task into sub-tasks. This makes it easier to see what happens and you might get interesting intermediary results. -??? "_Hint, Example_" +??? "_Hint_ **Example**" Let's say we want to find out all genes that contains a variant and all variants that are located within a gene. What do we want to do first? Take a look at the vcf file. That is the one that contains all the variants. Then look at the gff file, which contains the genes and other annotations. Finally, take a look at the DNA sequence. You will need to combine all three to answer the question. -??? "_Hint, Example, what do we need to get?_" +??? "_Hint_ **Example, what do we need to get?**" * Positions for SNPs and INDELs * Positions for genes and CDSs * Separation of variants (SNPs and INDELs) into two groups, inside and outside genes (and CDSs) @@ -68,12 +68,19 @@ A table with counted and sorted different genomic features in chromosome 4. #### *bonus result* SNPs sorted by number. Just like the coins on day one. +
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+## Hints, don't use unless necessary. -## Hints -??? "_bonus result example_ *A table with counted and sorted different genomic features in chromosome 4.*" + +??? "_bonus result example_ **A table with counted and sorted different genomic features in chromosome 4.**" ``` 1 chromosome 1 snoRNA