sortmerna showing problem of nucleotide length

Question

[ppnana]

I generated plant transcriptome data from Ion torrent S5 but even after doing fastx quality trimmer i performed sortmeRNA which is showing the issue "WARNING: At least one of the reads is shorter than 18 nucleotides, by default it will not be searched". Anyone having any suggestions what softwares can be used to analyse the same data. Thanks

Answer 1

[Nitin Narwade]

Is it just warning or is it interrupting program?

Because if it is warning you don't have to bother.

There is one more alignment-free Ribosomal RNA read removal tool: rRNAFilter; for metatranscriptomic data analysis.

Paper

Tool