leilaicruz
commented
3 years ago The documentation of the software package can be found here : https://transit.readthedocs.io/en/latest/index.html
- It can be easily installed via downloading, and use it through a GUI or can be used as a python package
- The GUI looks like :
Advantadges:
- Serve as an example pipeline that meet many of the requirements we want to reach for our pipeline regarding documentation , ease of use and maintenance. (I could explore the tool thanks of some emails exchange with the maintener)
- It has implemented relevant methods for us concerning the detection of genetic interactions due to significant variability of transposon counts between two conditions , as well as many more statistics on comparing different libraries.
Limitations:
- Currently the methods are to tackle Himar and Tn5 like transposon which are prokaryotic transposons and they have a different insertion profile from our Maize Ac/Ds transposon type.
- Furthermore our expermental conditions do not include sampling and sequence before our selection process , because we measure all "in vivo" , we dont have an "invitro" condition , where we generate also many reads. Because if we sequence before reseeding we wont have that much reads to align back to the genome. The only "in vitro" condition I could think of is measuring the reseed in a diploid where the selection on a gene deletion in one chromosome should play a lesser effect .
Current status:
- We are in touch with the developer/mainteners of the software (https://orca1.tamu.edu/essentiality/transit/) to see how can we adapt their software with our needs if possible.
- Keep exploring all the analysis methods they have in order to implement them as part of our pipeline.
- With the software you can visualize our reads counts on the genome
- And have some statistics per dataset:
Here a description on this software that captures many of the features that we would like to have in our pipeline concerning: