FAQs

1. How will the final results of any service (RNA-Seq, docking, simulation etc) will be provided to the user?

   Ans: The small files can be provided as attachment to the email. Large files (>8 MB) like processed count files or fastq files will be provided through a storage server.

2. What kind of plots/figures will be provided after RNA-Seq, ChIP-Seq and any other NGS related analysis?

   Ans: The users should mention their specific requirements in the beginning itself, whatever is agreed between the user and the bioinformatics facility will be provided on time. Generally publication quality figures including heatmaps for differentially expressed genes are provided after a successful RNA-Seq analysis.

3. What is the approximate time to finish a typical RNA-Seq analysis?

   Ans: The exact time depends on the number of samples and what types of analyses are needed by the user. Normally one week is enough for differential gene expression analysis for 5-10 samples. Again the approximate date of completion will be decided in the beginning itself before taking up the task.

4. I have some RNA-Seq data for control and disease condition. I am a biologist and I have no idea what to do with this data. Is this task suitable for a service?

   Ans: Normally when the users themselves are not sure what kind of analysis has to be done with their NGS data (RNA-Seq or any other data), it is better to go for collaboration rather than service. For services, we can entertain only specific requirements for which the users are sure what to do. Our bioinformatics staff will make a plan for how to do and make sure that it gets completed on time.

5. I am not sure if my requirement can be done as a service or not.

   Ans: For all the requirements where the users are not sure if it may be put as service or collaboration, please schedule a service meeting with one of our team members. After listening to your requirement only, we can suggest to you if it should be put up as a service or collaboration.

6. After completion of the service, is it possible for RGCB staff to teach me how to repeat the same analysis for other samples?

   Ans:No, our responsibility is only to provide the results mutually agreed. But RGCB conducts bioinformatics workshops/webinars on a regular basis, you can attend them. There are several online resources to learn them. At best, we can suggest you online resources, books, research/review articles etc for your learning.

7. Will you provide the references after the job is over?

   Ans:Yes, we try to use standard softwares which are published as software articles in reputed journals like Nucleic Acid Research, Bioinformatics etc. We will provide the proper references to include in your publication.

8. What are the deliverables for Protein-Protein docking

   Ans: The Docked Complex file (in PDB format) with their docking score from Cluspro/Zdock/Haddock. Protein-Ligand interactions map ( with probable H-bonds, Hydrophobic , Hydrophilic, Pi -Pi interactions etc as a datasheet) 3D Protein-Ligand interactions map (with interacting residues labeled in the image)

9. What are the deliverables from Protein-ligand docking

   Ans: The Docked Complex file (in PDB format) with their docking score from Autodock/Glide. 1D Protein-Ligand interactions map ( with probable H-bonds, Hydrophobic , Hydrophilic, Pi -Pi interactions etc as an Image) 3D Protein-Ligand interactions map (with H bonds interacting residues labeled in the image)

10. What are the deliverables of RNA-Seq analysis

    Ans: The output files filed from kallisto/sleuth/DeSeq2 pipeline Sample-wise RNA quantification data Differential expression Volcano Plot