.. (לתיקייה המכילה) | ||
What is the difference between a SNP and a sequencing error? | |
A sequencing error is an error that happens in the sequencing process - a certain base will be given as X when the actual base is really Y. Sequencing errors appear once in every ~100 bases (1% error rate). A SNP stands for Single Nucleotide Ploymorphism and is a single nucleotide difference from the reference genome. |
I have a problem uploading files to Galaxy. What should I do? Should I change my browser? | |
Since the Galaxy servers are not on our control there is nothing we can do other than to try a few times… It can happen that things will be slow or get stuck, but since files are small - it should not be that bad all the time. Different browsers have nothing to do with that.. |
Question 5 in part 2 - clarification | |
In this step you are asked to re run question 1 but in the context of RNA. Note that you are required to re run question 1 ONLY (using one tool only) and not the rest of the questions in RNA context . We didn't talk in class how exactly to run that program for RNA sequences, but you can easily discover this by a short look over the parameters of that program. Please be open minded :) |
How can the coloring in IGV display be set? | |
The coloring of variants in the coverage track (the one on the top that sums up all the reads) is done automatically. Every variant that has above 20% frequency in a certain base will be shown on the coverage track as shown in class. The coloring of the bases that are different from the reference in the alignment track (the reads themselves) can be change by clicking on the right mouse button and clicking on "Show mismatch bases" / "Show all bases". By default only bases that are different from the reference are colored. Hint: you don't need to change anything to get to the desired answers. All the coloring you need is set as default. |
How should I calculate the coverage? | |
The coverage should be calculated when taking into consideration the total reads that were mapped. You are not asked to refer to uniquely or non-uniquly mapped reads. |