Varun Shamanna

Varun Shamanna

I am Senior Bioinformatician at Central Research Laboratory, KIMS, Bengaluru

Location Bengaluru, INDIA


  • Hi, @DavidWalton Please use the Australian server as we have the workflow built in it and it will be easier to do.

  • @AnneM We have generated the nanopore sequences using the Midnight protocol. So the maximum read length will be 1300. There is an error in the transcript please use 1300.

  • @VerenaRas I have updated the workflow, please try it once again and you should be able to run it as per the tutorial video

  • @DavidRuidíasRomero Sorry, this was due to an update in the pangolin tool recently. Now I have updated the pipeline. You can import it once again and you should be able to run it as per the tutorial video.

  • @DavidWalton Please create a file called input.txt and upload the data once again and try.

  • If you have followed the steps properly the output file should have the order of the texts flipped. Please try once again and click on the eye icon in your output data to view the flipped text file.

  • Unlike short reads from the Illumina platform, the low-quality reads in nanopore sequencing will be filtered during the sequencing itself. So in nanoplot, you are just visualizing the statistics of good reads which includes the quality scores.

  • Yes, the dataset is created for this course and you will be using the uploaded collection of sequences in the upcoming steps.