Code Monkey home page Code Monkey logo

Comments (3)

adamd3 avatar adamd3 commented on July 19, 2024

Yes, it could be used for this purpose.

If you are not sure which bacterial species might be present, then I would suggest pseudo-aligning your FASTQ files to a database of ribosomal RNA genes for bacteria, since these are likely to be the most abundant transcripts. Put a representative set of rRNA sequences from different bacterial species in a single FASTA-format file for pseudo-alignment (use --aligner kallisto).

If you already have an idea of the species, you could just pseudo-align reads to the rRNA genes from that specific species.

You can trim adaptors from the reads and then remove any human-aligning reads first, as you suggested.
Then run the pipeline with the --skip_trimming flag, to avoid re-running the adaptor trimming step.

An example command might look like the below (where fasta_file contains the bacterial rRNA sequences):

nextflow run BactSeq --data_dir [directory_containing_fastq_files] --sample_file [sample_file] --ref_genome [fasta_file] --aligner kallisto --strandedness unstranded --skip_trimming --paired -profile [docker/conda]

See the example sample_file in the README for the format of this file. You can use -profile docker or -profile conda.

Let me know if you have any other questions.

from bactseq.

sirrgang avatar sirrgang commented on July 19, 2024

Thanks, you have a recommended source for ribosomal RNA genes for bacteria?

from bactseq.

sirrgang avatar sirrgang commented on July 19, 2024

I guess that could work here
https://www.arb-silva.de/fileadmin/silva_databases/current/Exports/SILVA_138.1_SSURef_tax_silva.fasta.gz

from bactseq.

Related Issues (3)

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.