---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
layout: post
title: lncRNA Identification - P.generosa lncRNAs using CPC2 and bedtools
date: '2023-05-02 08:29'
tags: 
  - lncRNA
  - Panopea generosa
  - Pacific geoduck
  - CPC2
  - bedtools
categories: 
  - 2023
  - Miscellaneous
---
After [trimming _P.generosa_ RNA-seq reads on 20230426](https://robertslab.github.io/sams-notebook/posts/2023/2023-04-26-FastQ-Trimming-and-QC-P.generosa-RNA-seq-Data-from-20220323-on-Mox.html) and then [aligning and annotating them to the Panopea-generosa-v1.0 genome on 20230426](https://robertslab.github.io/sams-notebook/2023/04/26/Transcript-Alignments-P.generosa-RNA-seq-Alignments-for-lncRNA-Identification-Using-Hisat2-StingTie-and-gffcompare-on-Mox.html), I proceeded with the final step of lncRNA identification. To do this, I used [Zach's notebook entry on lncRNA identification](https://zbengt.github.io/2023-04-20-LncRNA-Discovery/) for guidance. I utilized the annotated GTF generated by [`gffcompare`](https://ccb.jhu.edu/software/stringtie/gffcompare.shtml) during the [alignment/annotation step on 20230426](https://robertslab.github.io/sams-notebook/2023/04/26/Transcript-Alignments-P.generosa-RNA-seq-Alignments-for-lncRNA-Identification-Using-Hisat2-StingTie-and-gffcompare-on-Mox/). I used ['bedtools getfasta`](https://bedtools.readthedocs.io/en/latest/content/tools/getfasta/) and [`CPC2`](https://github.com/gao-lab/CPC2_standalone) with an aribtrary 200bp minimum length to identify lncRNAs. All of this was done in a Jupyter Notebook (links below).

Jupyter Notebook (GitHub):

- [20230502-pgen-lncRNA-identification.ipynb](https://github.com/RobertsLab/code/blob/master/notebooks/sam/20230502-pgen-lncRNA-identification.ipynb)

Jupyter Notebook (NB Viewer):

- [20230502-pgen-lncRNA-identification.ipynb](https://nbviewer.org/github/RobertsLab/code/blob/master/notebooks/sam/20230502-pgen-lncRNA-identification.ipynb)


<iframe src="https://nbviewer.org/github/RobertsLab/code/blob/master/notebooks/sam/20230502-pgen-lncRNA-identification.ipynb" width="100%" height="1000" scrolling="yes"></iframe>

---

# RESULTS

Some very brief "stats":

Total P.generosa transccripts ID's by HiSat2/Stringtie: `79,269`

Total P.generosa lncRNA ID'd by CPC2 (>= 200bp): `13,606`

Percentage of transcripts which are lncRNAs: `17%`

Output folder:

- [20230426-pgen-HISAT2-stringtie-gffcompare-RNAseq/](https://gannet.fish.washington.edu/Atumefaciens/20230426-pgen-HISAT2-stringtie-gffcompare-RNAseq/)

  #### lncRNA GTF
  
    - [20230502-pgen-lncRNA-IDs.gtf](https://gannet.fish.washington.edu/Atumefaciens/20230426-pgen-HISAT2-stringtie-gffcompare-RNAseq/20230502-pgen-lncRNA-IDs.gtf) (2.2M)

    - MD5: `9adb7efc18fe1bfedcad24c86da1161f`