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  • earonesty
    replied
    actually there's a bug in bowtie ... a race condition that can make it unreliable. you should not use fifo's unless you used the patched version that supports them

    An ultrafast memory-efficient short read aligner. Contribute to earonesty/bowtie development by creating an account on GitHub.

    Leave a comment:


  • westerman
    replied
    FYI, zcat is often a shortcut to 'gunzip -c'

    Also under BASH you should be able do something like:

    bowtie -1 <( zcat file1.gz ) -2 <( zcat file2.gz )

    or in the original posters question

    bowtie2 -U <( zcat file.gz )

    Leave a comment:


  • earonesty
    replied
    Originally posted by dsenalik View Post
    I needed to add a "-c" to that command, otherwise gunzip will delete the original compressed file, i.e.
    Code:
    mkfifo file1.fifo
    mkfifo file2.fifo
    gunzip -c file1.gz > file1.fifo &
    gunzip -c file2.gz > file2.fifo &


    this patch fixes fifo support, and also adds built-in gzip support to bowtie 1.0 (which remains the fastest, fastq->sam program out there)

    An ultrafast memory-efficient short read aligner. Contribute to earonesty/bowtie development by creating an account on GitHub.

    Leave a comment:


  • dsenalik
    replied
    I needed to add a "-c" to that command, otherwise gunzip will delete the original compressed file, i.e.
    Code:
    mkfifo file1.fifo
    mkfifo file2.fifo
    gunzip -c file1.gz > file1.fifo &
    gunzip -c file2.gz > file2.fifo &

    Leave a comment:


  • gringer
    replied
    Originally posted by earonesty View Post
    # HOW to add GUNZIP support to ANY program that doesn't have it:

    mkfifo file1.fifo
    mkfifo file2.fifo
    gunzip file1.gz > file.fifo &
    gunzip file2.gz > file.fifo &
    bowtie -1 file1.fifo -2 file2.fifo
    In many cases this will work, but not all cases. This doesn't work for programs that attempt to seek through files (low-memory fastq randomisation being one example that I've recently seen).

    Leave a comment:


  • yumtaoist
    replied
    Originally posted by earonesty View Post
    # HOW to add GUNZIP support to ANY program that doesn't have it:

    mkfifo file1.fifo
    mkfifo file2.fifo
    gunzip file1.gz > file.fifo &
    gunzip file2.gz > file.fifo &
    bowtie -1 file1.fifo -2 file2.fifo
    Thank You Very Much!

    This is very useful!

    Leave a comment:


  • earonesty
    replied
    # HOW to add GUNZIP support to ANY program that doesn't have it:

    mkfifo file1.fifo
    mkfifo file2.fifo
    gunzip file1.gz > file.fifo &
    gunzip file2.gz > file.fifo &
    bowtie -1 file1.fifo -2 file2.fifo

    Leave a comment:


  • yumtaoist
    started a topic Bowtie2 cannot read gzip format files

    Bowtie2 cannot read gzip format files

    Hey, everyone!

    The help document of bowtie2 have said that the files of reads could be gzip'ed.

    When I use the paired reads and try the argument ( -1 <m1> -2 <m2>), the bowtie2 can read the gzip'ed files.

    However, if I use the gzip'ed unpaired reads and apply the argument (-U <r>), the bowtie2 suggest that "Error: reads file does not look like a FASTQ file". The gzip'ed file can not be recognized.

    Does anyone have come up with this problem?

    Thank You!

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