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I am trying to convert BAM files from Ion Amplicon sequencing to FASTQ files. I am using Google Collaboratory. I will be using the FASTQ files in R for the pipeline DADA2. Any help would be greatly appreciated.

zx8754
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Nicole_B
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  • How are you using Google colab for this? Are you uploading BAM files? Are they already available within Google colab. I would advise against using colab for processing of raw sequencing data. For example, when installed locally, the ever useful `bedtools` has a utility to convert BAM to FASTQ files. – Maurits Evers Nov 04 '21 at 09:27
  • In R maybe this will help: https://support.bioconductor.org/p/119522/ – Lucas Nov 04 '21 at 09:31
  • I will have to upload the BAM files from my computer, I'm not certain how to use Google Colab. It's just the only coding platform I've been exposed to. – Nicole_B Nov 04 '21 at 09:42
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    @Nicole_B In that case I *really* advise *against* using Google colab. File sizes of BAM and FASTQ files can become fairly large, which would create a lot of upload/download traffic. Better to install one of the standard tools (like `bedtools`, `samtools` etc.) and work on those file locally from the command line (no coding necessary). Chances are that you'll be needing some of those standard tools in your downstream bioinformatics work again. – Maurits Evers Nov 04 '21 at 09:46

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