---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
layout: post
title: Data Wrangling - FastA Subsetting of Pgenerosa_v070.fa Using samtools faidx
date: '2019-06-25 13:04'
tags:
  - samtools
  - faidx
  - Panopea generosa
  - geoduck
  - Pgenerosa_v070.fa
  - v070
categories:
  - 2019
  - Miscellaneous
---
Steven asked to subset the [Pgenerosa_v070.fa](http://owl.fish.washington.edu/halfshell/genomic-databank/Pgenerosa_v070.fa) (2.1GB) in this [GitHub Issue #705](https://github.com/RobertsLab/resources/issues/705). In that issue, it was determined that a significant portion of the sequencing data that was assembled by Phase Genomics clustered in "scaffolds" 1 - 18. As such, Steven asked to subset just those 18 scaffolds.

This was done by using the `samtools faidx` program.

Process is documented in the following Jupyter Notebook (GitHub):

- [20190625_swoose_pgen_v070_scaffolds.ipynb](https://github.com/RobertsLab/code/blob/master/notebooks/sam/20190625_swoose_pgen_v070_scaffolds.ipynb)


---

# RESULTS

Output folder:

- [20190625_pgen_v070_scaffold_subsetting/](https://gannet.fish.washington.edu/Atumefaciens/20190625_pgen_v070_scaffold_subsetting/)

FastA (914MB):

- [20190625_pgen_v070_scaffold_subsetting/Pgenerosa_v070.18.fa](https://gannet.fish.washington.edu/Atumefaciens/20190625_pgen_v070_scaffold_subsetting/Pgenerosa_v070.18.fa)

FastA Index:
- [20190625_pgen_v070_scaffold_subsetting/Pgenerosa_v070.18.fa.fai](https://gannet.fish.washington.edu/Atumefaciens/20190625_pgen_v070_scaffold_subsetting/Pgenerosa_v070.18.fa.fai)