Snehal Karpe

4 Questions 14 Answers 0 Followers

Questions related from Snehal Karpe

Which is the best assembler for 150bp paired end RNAseq data from around 300MB sized eukaryotic genome?

I was hoping to use Trinity, but it does not allow kmer size more than 32. Based on few expert suggestions, the ideal kmer size here should be between 75-100. Will Trinity based assembly be of...

09 April 2018 8,251 5 View

Which is the best method of doing transcriptome assembly of samples of various tissues and also those collected from different geographical locations?

Consider samples from tissues A and B of a species X collected from geographical location 1 and samples from the same tissues A and B collected from geographical location 2. If we are to do...

19 January 2018 4,420 4 View

What are the best practices to model structure of an insect olfactory / odorant receptor (computationally) according to you?

Kindly suggest your views on the topic. Please provide references wherever possible.

19 August 2017 5,262 7 View

Which is the best free genome annotation editor that can give output in gff3/gtf file/s compatible with RNAseq analysis tools (e.g. STAR)?

I need to include new genes, pseudogenes and modify gene/intron-exon boundaries of few genes in the available annotations from NCBI. GFF3 files follow complex format which is very difficult to...

30 September 2015 3,189 10 View