Hi,
I know Bowtie supports piping (although not so convenient to use for paired-end reads), and I am wondering if TopHat does the same. I tried something like "gzip -dc $fq | tophat $genome -" but it doesn't work. Did I do anything wrong? Or if there are other ways to run TopHat without decompressing the sequence files first? Please feel free to share your tips/suggestions. Thanks a lot!
-- Leo
I know Bowtie supports piping (although not so convenient to use for paired-end reads), and I am wondering if TopHat does the same. I tried something like "gzip -dc $fq | tophat $genome -" but it doesn't work. Did I do anything wrong? Or if there are other ways to run TopHat without decompressing the sequence files first? Please feel free to share your tips/suggestions. Thanks a lot!
-- Leo
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