.. (לתיקייה המכילה) | ||
Where can I find the % of uniquely mapped reads in order to compute the average coverage? | |
The summary of the mapping process is given by step 4 in the instruction (SAMtools -> IdxStats), but this tool doesn't differentiate between uniquely- and multi-mapped reads. So you can assume that all mapped reads are uniquely mapped. |
How can fold-change be a negative value? | |
Fold-change, defined as the ratio between the average of condition 1 values and the average of condition 2 values, is usually used in log scale (meaning the ratio is log-transformed) - so it can be negative. Values that were originally above 1 are positive and values that were originally below 1 are negative. |
Q2 - If all the mapped reads are uniquely mapped, should we consider %uniquelly mapped reads as 100% and use this number in the formula? | |
In this case, you should use 1 as a substitution of %uniquelly mapped reads in the formula. |