get an error "Expecting at least 3 words line 1 of /dev/stdin got 1" making bigBed
I tried to pipe into bedToBigBed but I got an error:
cat test.bed | cut -f1-3 | sort -k1,1 -k2,2n | bedToBigBed /dev/stdin chrom.sizes test.bb
Expecting at least 3 words line 1 of /dev/stdin got 1
When I do each step separately everything goes fine!
Does anybody know what is the problem?
2 answers
Try stdin instead of /dev/stdin
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Ram
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written
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Pierre Lindenbaum
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written
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Pierre Lindenbaum
a dash '-' instead of stdin ?
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Pierre Lindenbaum
Some conversion tools in UCSC don't support reading from stdin as they need to pass through the input file multiple times. I'm pretty sure this the case for bedGraphToBigWig and I suspect it is the same for bedToBigBed. I don't have a reference at hand but google around to see if this is the case.
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