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De novo assemble RNA-seq sequence

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AI-generated summary
The document outlines a workflow for analyzing RNA-seq data from a new coronavirus subgenus to investigate potential changes in protease. The steps include setting up a conda environment, fetching RNA-seq data, performing quality checks using FastQC and Fastp, assembling the cleaned reads with Trinity, and conducting BLAST searches to identify sequences of interest. Key steps include: 1. **Environment Setup**: Create and activate a conda environment with necessary bioinformatics tools. 2. **Data Fetching**: Use SRA tools to download and prepare the RNA-seq data. 3. **Quality Control**: Assess and clean the data using FastQC and Fastp. 4. **Assembly**: Assemble the cleaned data using Trinity. 5. **BLAST Analysis**: Create a BLAST database from the assembled sequences and run BLAST searches against a query sequence. 6. **Sequence Extraction**: Extract specific sequences from the Trinity assembly for further analysis. The document also mentions using TransDecoder for predicting coding regions and performing additional BLAST analyses on predicted sequences.

Intro#

A research paper published on biorxiv determined a new coronavirus subgenus, I would like to figure out is there any changes on protease. However, the sequence data has not been publish.

Fortunately, the similar sequence is do available on NCBI, unfortunately, only RNA-seq data is available.

So I need to assemble the RNA-seq reads first, and BLAST the sequence I need with the assembled data.

TL;DR#

  1. Setup the environment with conda:

  2. Fetch the data:

  3. Data quality check

  4. Quality control using fastp

  5. Data quality check (post-cleaning data)

  6. Assemble with Trinity

  7. Check the Trinity result:

  8. BLAST sequence of interest

    1. Put your sequence in query.fasta.

    2. Make BLAST database and run:

  9. Check the BLAST result:

  10. Extract the sequence from trinity.Trinity.fasta

Tail#

  1. You can also blast with the Predicted sequence:

  2. Make BLAST database and run:

此文由 Mix Space 同步更新至 xLog
原始链接为 https://xxu.do/posts/academic/De-novo-assemble-RNA-seq-sequence

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