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,
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.