It was the type=bedgraph line that was causing the problems so I deleted it..
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It seems the type=bedGraph is important in the file! So I have it at the top of my sorted bedGraph. However, when I then do the bedGraphToBigWig conversion I still get an error: Expecting at least 3 words line 1 of sample_CO115_sorted.bedGraph got 1
How do I overcome this?
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Could I just suggest that every time you change your bedGraph file, you post ten lines of it and the exact command you used along with your new question? This will reduce the required back-and-forth by about two thirds from the look of things.
So guess what we need from you to answer your most recent question.
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This is the first 10 lines of the (sorted) bedGraph:
type=bedGraph
chr1 10469 10469 100
chr1 10471 10471 100
chr1 10484 10484 100
chr1 10489 10489 100
chr1 10493 10493 100
chr1 10497 10497 100
chr1 10525 10525 60
chr1 10542 10542 60
chr1 10563 10563 60
I use this code to convert to a bigWig:
bedGraphToBigWig sample_CO115_sorted.bedGraph hg19.chrom.sizes CO115.bw
I get this error:
Expecting at least 3 words line 1 of sample_CO115_sorted.bedGraph got 1
If I remove the type=bedGraph from the bedGraph file I get an unreadable bigWig.
Thanks for your help.Last edited by Hparker; 07-05-2015, 10:57 PM.
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I have made sure the first line of the bedGraph file now reads:
track type=bedGraph
I no longer get the error but the bigWig file does not seem right, first few lines shown below:
&¸èà
X¡jµÏ0ÄÄÚ≠Òp
T–pD)æ(úùæ¡ÎŸ†-⁄Nh‚Ä≤Ç‚Æ‚‰
z˚‰äöÂ(Ê≤Âҋ†5ıÂ.ÊÄjÊ[Ê
ó5Ê7ÊY@ëå*xchr1=C€chr10õchr114 chr12˜j˙chr13VZ›chr14$fchr15@Åchr16A¥bchr17*÷chr18 @]ßchr19
ó<Üchr2çÌ~chr20p±¡chr21
ggfichr22vÿchr3ïÕchr4d»dchr5<å»
chr6;3
I used this code:
bedGraphToBigWig sample_CO115_sorted.bedGraph hg19.chrom.sizes CO115.bw
...and the bedGraph first 10 lines:
track type=bedGraph
chr1 10469 10469 100
chr1 10471 10471 100
chr1 10484 10484 100
chr1 10489 10489 100
chr1 10493 10493 100
chr1 10497 10497 100
chr1 10525 10525 100
chr1 10542 10542 100
chr1 10563 10563 100
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Also, based on the lines you posted, "wiggle" might be a more appropriate format than "bedGraph" for the plaintext version of your data anyway.
Code:track type=bedGraph chr1 10469 10469 100 chr1 10471 10471 100 chr1 10484 10484 100 chr1 10489 10489 100 chr1 10493 10493 100 chr1 10497 10497 100 chr1 10525 10525 100 chr1 10542 10542 100 chr1 10563 10563 100
Code:track type=wiggle_0 variableStep chrom=chr1 10469 100 10471 100 10484 100 10489 100 10493 100 10497 100 10525 100 10542 100 10563 100
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