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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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