Need to sortout my differential expression gene list into various types of coding and noncoding RNAs (lnc RNA, SnoRNA,miRNA, piRNA etc.) of RNAseq? Please suggest me the database or methods to do so..... .
Hello
It depends what package you used to get your DEG list. If you used Tuxedo suit, at the Cuffmerge step, you would have another extra column named class code. It has 3 codes of i, u & x. These are for identification of novel transcripts and non-codings from known coding sequences.
If you have a limited number of unknown sequences, you may try using the NONECODE database to locate them in the genome to see if they are a real LNC RNA.
MiRNAs usually could not be detected with a normal RNAseq library prep, so dont look for them!
nice harshraj,
nice to get answer from you, but i am asking about already available database from where i can get list of already available types of RNA, and then i will be in a position of making match with my list of available species.
Hello,
If you want to annotate list of genes you can do it in different ways:
- you can find type of the genes using biomart of Ensembl manually or using R packages.
- you can also extract the type of your interested genes from gtf or Genecode files.
To Ali Javadmanesh ,
thank you ali, thank you so much for your reply.
we need further clarification about all the three codes i,u and x.
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