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  • BAM file search

    Sorry if this has already been answered somewhere else, perhaps I'm searching the wrong terms

    I'm beginning a metagenomics/metatranscriptomics project regarding freshwater bacterial populations. I've received my data in the form of a .bam file, which I have already sorted and indexed using samtools. I am interested in searching the data for specific protein sequences, but am unsure how to go about doing this. Is there a simple way I could BLAST this file (or some similar search tool) for these sequences?

    I also received a .fastq file, so maybe I will need to convert this to a .fasta and use it as a library for stand-alone BLAST?

    Thanks for your help

  • #2
    Realign the fastqs to the desired DNA sequences. (I take it you can't easily figure out where they are in relation to whatever your fastq was originally aligned to?) You'll get a little bit of false positives, as the software will try and force some reads to align that really don't belong, but it should work well enough.

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    • #3
      Do you have any program suggestions for using the fastq file? Otherwise I think I will need to convert it to a fasta file.

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