Transcriptome upstream script introduction

The purpose of this part of the code is to help users pre-process their own transcriptome raw data on their own machine. The output of this script is the gene count and TPM file. These output results can be input by the user as an input file to the "upload own data" section of FishCODE's online transcriptome analysis.

Considering the large-scale computing power required for the pre-processing of omics raw data, this series of processing scripts currently only supports Linux or Linux-like systems. More local software supported by the system are in our development list, so please pay attention to our webpage. It is worth noting that although FishCODE focuses on the analysis of fish omics data, this series of scripts is a general omics data processing flow, and users can use this processing flow to process any omics annotations (at least genome and gff files) Species.

Code download

Getting started

Before you start

The pp.conf file records the absolute paths of the dependent software mentioned below. Before you start you must configure this file and replace the execution path of the software with the absolute path to the software on your server!

First: create database index for analysis

Dependent software: gffread, salmon 1.4.0, bedtools v2.26.0, mashmap

$ bash First_bulid_index.sh ./build_faidx_example/GCF_901000725.2_fTakRub1.2_genomic.fna ./build_faidx_example/GCF_901000725.2_fTakRub1.2_genomic.gff 30

Note: 1. Your genome and corresponding annotation files must be in the same folder. 2. All the following working directories default to the decompressed directory.
3. The first parameter is the genome location, the second parameter is the gff file location, and the third parameter is the number of threads

Second: quality control

Dependent software: NGSQCToolkit_v2.3.3 (IlluQC.pl)

$ bash filter.sh 792045 SRR17641338

Note: The first parameter is the name of the upper folder where fastq.gz is located, or the project name, and the second parameter is the prefix of fastq.gz. For the specific file structure, please refer to the compressed package. The user must create a project under the parent directory 00_data, and store the sequencing files to be processed under the project name. "./00_data/projectname/*fastq.gz"

Third: count

Dependent software: salmon 1.4.0

$ bash salmon.sh 792045 SRR17641338 ./build_faidx_example/GCF_901000725.2_fTakRub1.2_genomic.fna ./build_faidx_example/GCF_901000725.2_fTakRub1.2_genomic.gff

Note: The first parameter is the project name of the second step, the second parameter is the prefix of fastq.gz, the third parameter is the genome location, and the fourth parameter is the location of the gff file (note that the location of this genome and annotation file must Strictly the input genome and gff file path for the first step)

Others

1. The output result of the third step will be in 01_result/792045/SRR17641338_quant/ under the same directory

2. All directory structures and demonstration data examples are included in the compressed package, allowing users to try it easily.

3. In order to facilitate users to generate transcriptome data corresponding to the species included in FishCODE, we provide a download package of the genome and annotation files of FishCODE's 35 fish species in the "Help->Usage->gene information" section.