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tderrien / FEELnc

FEELnc : FlExible Extraction of LncRNA
GNU General Public License v3.0
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Issues about candidate_lncRNA_classes.txt #20

Closed EternalVoice closed 6 years ago

EternalVoice commented 6 years ago

Hi, @tderrien @vwucher I got TWO questions. 1)How can extract FASTA format sequence by final output file-candidate_lncRNA_classes.txt combined with my genome.fa? It seems that the classifier output file only contian distance, how can I get its start_position & end_position? 2) Is there any downstream tools for further analysis? I am stuck in there. I did find lncRNAs using FEELnc, but, so, thanks! But, I have to further analyse these lncRNAs. Your reply will be appreciated!

Vaney

tderrien commented 6 years ago

Hi Vaney, Tx for your feedback. 1/ The start and end coordinates of the lncRNAs should be annotated in the .gtf file following the FEELnc_codpotl module. To get the FASTA sequences of transcripts annotated in .gtf, there are many tools to do that. If you want, you can use a custom script gtf2fasta.pl available here: https://github.com/tderrien/IGDR/blob/master/script/gtf2fasta.pl 2/ Good question :-) Very difficult to answer depending on your biological questions e.g. finding differentially expressed lncRNAs, conserved lncRNAs, co-expressed lncRNAs:mRNAs... Best,

Thomas