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  • Aligning multiple paired-end files with subread

    Hi all,

    Is there anyone out there who knows whether it's possible to align multiple paired-end sequencing fastq files with subread at the same time? For example, we have paired-end sequencing data for 148 samples which we want aligning with subread. We would like to avoid having to set this running sample by sample one at a time. Is there a way to run it in batch for all these samples contained in the same directory? R or command line version solutions would be appreciated, we could use either.......

  • #2
    The align() function in Bioconductor package Rsubread allows you to provide multiple input files for alignment at the same time:

    Alignment, quantification and analysis of RNA sequencing data (including both bulk RNA-seq and scRNA-seq) and DNA sequenicng data (including ATAC-seq, ChIP-seq, WGS, WES etc). Includes functionality for read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. Can be applied to all major sequencing techologies and to both short and long sequence reads.


    The align() function is an R wrapper function for the 'subread-align' command in SourceForge Subread package. If you run 'subjunc' command, you can use the subjunc() function in Rsubread as well.

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