Hello
We analyse Solid 5500 RNA seq reads. I used tophat2 for the alignment. We performed first the mapping with different options for the insert size and std deviation
-r/--mate-inner-dist <int> This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments selected at 300bp, where each end is 50bp, you should set -r to be 200. The default is 50bp.
--mate-std-dev <int> The standard deviation for the distribution on inner distances between mate pairs. The default is 20bp.
Whatever the size / std dev was, we obtained exactly the same results, meaning these options seems not to be considered.
Please let me know if someone else already saw that and how to fix it. Thanks a lot for your time
We analyse Solid 5500 RNA seq reads. I used tophat2 for the alignment. We performed first the mapping with different options for the insert size and std deviation
-r/--mate-inner-dist <int> This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments selected at 300bp, where each end is 50bp, you should set -r to be 200. The default is 50bp.
--mate-std-dev <int> The standard deviation for the distribution on inner distances between mate pairs. The default is 20bp.
Whatever the size / std dev was, we obtained exactly the same results, meaning these options seems not to be considered.
Please let me know if someone else already saw that and how to fix it. Thanks a lot for your time
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