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  • lwhitmore
    replied
    Default bowtie

    Hi I am just wondering if you run bowtie with -v 0 (meaning no mismatches are allowed in the alignment) and -a (meaning mulitple alignments are allowed) is the last column the number of times the read maps to the genome? 0 indicating that the alignment is unique?

    Leave a comment:


  • swbarnes2
    replied
    I'm pretty sure that bowtie's default alignment will output one line for each aligned read, and no lines for each unaligned read, so you could do a wc -l on the file, and just count how many lines there are, and that's how many reads aligned.

    Leave a comment:


  • psurana
    replied
    Originally posted by DZhang View Post
    Hi psurana,

    This does not answer your question directly but may help you out: Bowtie can output alignment in the sam format. So if you can not find a solution to your problem, you may redo the alignment with option -S (or --sam)

    Douglas
    www.contigexpress.com
    Thanks, I might try that.

    Leave a comment:


  • DZhang
    replied
    Hi psurana,

    This does not answer your question directly but may help you out: Bowtie can output alignment in the sam format. So if you can not find a solution to your problem, you may redo the alignment with option -S (or --sam)

    Douglas

    Leave a comment:


  • psurana
    replied
    Originally posted by fabrice View Post
    samtools flagstat a.bam
    I have the bowtie output in the default format not the sam format. Is there a way to convert the already existing bowtie default output to sam format which I could then convert to bam of course.

    Thanks

    Leave a comment:


  • fabrice
    replied
    samtools flagstat a.bam

    Leave a comment:


  • psurana
    started a topic Bowtie Output Information

    Bowtie Output Information

    Does anyone know how to find out % aligned reads from a bowtie output file? Is there a command to do it? Is it there somewhere in the file? I did not save this information for my output files and would like to get it now.

    Thanks,
    Priyanka Surana

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    Multiomics Techniques Advancing Disease Research
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    New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

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