feelnc

Version:: 0.2
Category:: bio
Cluster:: Loki

Author / Distributor

https://help.rc.ufl.edu/doc/FEELnc

Description

This document gives a technical description of the FEELnc pipeline in order to annotate long non-coding RNAs (lncRNAs) based on reconstructed transcripts from RNA-seq data (with/without a reference genome). For a more general overview of RNAs annotation using RNASeq and FEELnc advantages, you could point to the FEELnc paper.

Documentation

Usage:
   FEELnc_filter.pl -i candidate.gtf -a mRNA.gtf > candidate_lncRNA.gtf

Options:
 General:
       --help                      Print this help
       --man                       Open man page
       --verbosity                 Level of verbosity 0, 1 and 2 [default 1]

 Mandatory arguments:
       -i,--infile=file.gtf        Specify the GTF file to be filtered (such as a cufflinks transcripts/merged .GTF file)
       -a,--mRNAfile=file.gtf      Specify the annotation GTF file to be filtered on based on sense exon overlap (file of protein coding annotation)

 Filtering arguments:
       -s,--size=200               Keep transcript with a minimal size (default 200)
       -b,--biotype                Only consider transcript(s) from the reference annotation having this(these) biotype(s) (e.g : -b transcript_biotype=protein_coding,pseudogene) [default undef i.e all transcripts]
       -l,--linconly               Keep only long intergenic/interveaning ncRNAs [default FALSE]
       --monoex=-1|0|1             Keep monoexonic transcript(s): mode to be selected from : -1 keep monoexonic antisense (for RNASeq stranded protocol), 1 keep all monoexonic, 0 remove all monoexonic   [default 0]
       --biex=25                   Discard biexonic transcripts having one exon size lower to this value (default 25)

 Overlapping specification:
       -f,--minfrac_over=0         Minimal fraction out of the candidate lncRNA size to be considered for overlap [default 0 i.e 1nt]
       -p,--proc=4                 Number of thread for computing overlap [default 4]

 Log output:
       -o,--outlog=file.log                Specify the log file of output which [default infile.log]

Examples/Usage

List available modules:
```
$ module avail feelnc
```
Load the feelnc module:
```
$ module load bio/feelnc/0.2
```
Check the loaded modules:
```
$ module list
```
Unload the feelnc module:
```
$ module unload bio/feelnc/0.2
```

Installation

Source code is obtained from feelnc