Hi I am trying to pipe the output .wig format of igvtools count to wigToBigWig to convert to .bw format.
Here is my code:
igvtools count -w 10 -f median $file stdout hg19 | wigToBigWig stdin hg19.chrom.sizes ${name}.bw
I have also tried:
igvtools count -w 10 -f median $file stdout hg19 | wigToBigWig -clip stdin hg19.chrom.sizes ${name}.bw
igvtools 'count' and wigToBigWig work well separately without the pipe, so I am unsure of why they don't work with the pipe?
UCSC tools wigToBigWig should work by taking stdin based on other posts I've seen: http://seqanswers.com/forums/showthread.php?t=8448
The only error message I am getting is this:
Unrecognized line 1 of stdin: Using system JDK. Done
Otherwise everything else looks normal. Please let me know if anyone knows what's going on! Thank you very much,
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written
by
jennxyzhang •
try:
igvtools count -w 10 -f median $file stdout hg19 | grep -v "Using system JDK" | wigToBigWig stdin hg19.chrom.sizes ${name}.bw
another option:
edit the script igvtools try to replace https://github.com/igvteam/igv/blob/6960eaf1b04d5932429060bd6ff4b0f053c4be1e/scripts/igvtools#L10
echo "Using system JDK."
with
echo "Using system JDK." >&2
Furthemore, verify that the output of
igvtools count -w 10 -f median $file stdout hg19 | head
is wig
Thank you very very much for your suggestions! Unfortunately I'm still getting that same pop up "Unrecognized line 1 of stdin:" I'll stick with running these two commands separately.
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