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
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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 )
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Originally posted by dsenalik View PostI 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)
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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 &
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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
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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
This is very useful!
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# 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
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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!Tags: None
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