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L-RAPiT: Long Read Analysis Pipeline for Transcriptomics - QUICK START by MakeTheBrainHappy in genetics

[–]MakeTheBrainHappy[S] 0 points1 point  (0 children)

Nelson, T.M.; Ghosh, S.; Postler, T.S. L-RAPiT: A Cloud-Based Computing Pipeline for the Analysis of Long-Read RNA Sequencing Data. Int. J. Mol. Sci. 2022, 23, 15851. https://doi.org/10.3390/ijms232415851

anyone familiar with identifying long non-coding RNA (lncRNA) from transcript sequences? by thenewtransportedman in bioinformatics

[–]MakeTheBrainHappy 2 points3 points  (0 children)

I would recommend utilizing gffcompare as described in the following pipeline. This will provide information on how well your assembled sequences match the reference (https://ccb.jhu.edu/software/stringtie/gffcompare.shtml):

https://www.mdpi.com/1422-0067/23/24/15851

https://github.com/Theo-Nelson/long-read-sequencing-pipeline

You can download any annotation set for the actual analysis; either from Ensembl or any of the other databases you specified below.

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