FEELnc
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tderrien
FEELnc : FlExible Extraction of LncRNA
Hello, I am trying to run `FEELnc_filter.pl` and I encounter the `Parser::parseGTF => Data Structure returns an empty hash` error as follows: ``` bash-4.2# FEELnc_filter.pl -i d_magna.filtered.gtf -a daphnia_genome.gtf -b...
Hello there, I'm running the FEELnc_filter module in two approaches, as follows: `-i taco-new-assembly.gtf -a gencode.v40.primary_assembly.annotation.gtf -b transcript_biotype=protein_coding --monoex=0 -p 16 -o FEELnc_filter-1stStranded.log > 1st-strandedTFBfiltered.gtf &` and `-i taco-new-assembly.gtf -a...
my command line: ``` FEELnc_codpot.pl -i candidate_lncRNA.gtf -a stringtie_merged.gtf -g /mnt/data1/project/HYHjellyfish20230508/0_genome.nextpolish/genome.nextpolish.fasta --mode=intergenic ``` ``` Possible precedence issue with control flow operator at /mnt/data/software/miniconda3/envs/feelnc/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805. You do not have specified...
Hi, I would just like to understand the output of "FEELnc_classifier.pl". The parameter passed for the identification of lncRNA interaction is: "#Minimal window size : 1000 #Maximal window size :...
Hello! When installing FEELnc via conda, the script `FEELnc_tpLevel2gnLevelClassification.R` fails with a syntax error: miniconda3/envs/feelnc/bin/FEELnc_tpLevel2gnLevelClassification.R: 9: Syntax error: "(" unexpected Cloning the repository directly avoids this syntax error, but I...
Hello there! I noticed that the `$proc` argument can be passed to `FEELnc_codpot.pl` to then run `KmerInShort` with a number of processes equal to `$proc`. https://github.com/tderrien/FEELnc/blob/8ea728ebbe0b17a090fa23c8361168f1729fb7f7/scripts/FEELnc_codpot.pl#L90-L114 However, it is not...
Hi, I want to know if we can identify all the overlapping lncRNAs. The lncRNA of my interest overlaps with a gene, and when I filter the lncRNAs using two...
Hi there, I’m a molecular biologist and I’m a bit confused about something we did. We used the FEELnc tool to predict lncRNA, and in the output files, we see...
