[jwfoley]

Also, based on the lines you posted, "wiggle" might be a more appropriate format than "bedGraph" for the plaintext version of your data anyway.

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

is more efficiently stored as

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

(assuming you meant for your values to span 1 position each instead of 0 positions each, which is how they're interpreted in bedGraph format since it's zero-based, half-open)

[Hparker]

It's working in IGV! Thanks for all your help!

[GenoMax]

bigWig files are an indexed binary format. You will not be able to view them in a terminal. Try the file at UCSC.

[Hparker]

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

[GenoMax]

track type=bedGraph

is the full declaration required (word track is needed, I have edited my previous posts to reflect this). Can you try again?

[Hparker]

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.

[jwfoley]

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.

[Hparker]

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?

[Hparker]

It was the type=bedgraph line that was causing the problems so I deleted it..

[GenoMax]

Is that the last line in your file (a blank line perhaps)?

$ wc -l sample_CO115.bedGraph

[Hparker]

Because I am now getting these errors:
Expecting at least 3 words line 1321892 of sample_CO115.bedGraph got 1

This is quite time consuming going through all the data to find where there are gaps.. is there a way of doing this in unix?

Thanks a lot for your help!

[GenoMax]

You can edit manually (TextEdit or TextWrangler on Mac).

[Hparker]

Ah great! Can you edit it manually? Or is there code?

[GenoMax]

type=bedGraphchr7 12784 12784 100
chr7 12948 12948 100
chr7 12962 12962 0
chr7 13071 13071 100
chr7 13107 13107 100
chr7 13119 13119 100
chr7 19750 19750 50
chr7 19751 19751 100
chr7 19771 19771 50
chr7 19772 19772 0

It appears to have type=bedGraph at the beginning of the file?

Right but it has to be on a separate line by itself.

Edit so the file has a return:

type=bedGraph
chr7	12784	12784	100
chr7	12948	12948	100

[Hparker]

type=bedGraphchr7 12784 12784 100
chr7 12948 12948 100
chr7 12962 12962 0
chr7 13071 13071 100
chr7 13107 13107 100
chr7 13119 13119 100
chr7 19750 19750 50
chr7 19751 19751 100
chr7 19771 19771 50
chr7 19772 19772 0

It appears to have type=bedGraph at the beginning of the file?