Wig to Bigwig - UCSC software - error in "item ends"

Question

[matteo.zoia]

I want to produce a BIGWIG file from a WIG one using the wigToBigWig tool provided by UCSC.

I type my script :

./wigToBigWig H3K4me1ESCRep1JWH11c.wig mm9.chrom.sizes.txt myBigWig.bw

Got the Error:

line 701578 of H3K4me1ESCRep1JWH11c.wig: chromosome chr2 has 181748087 bases, but item ends at 181748225 
line 1323736 of H3K4me1ESCRep1JWH11c.wig: chromosome chr4 has 155630120 bases, but item ends at 155630325
line 1615096 of H3K4me1ESCRep1JWH11c.wig: chromosome chr7 has 152524553 bases, but item ends at 152524750
line 3011902 of H3K4me1ESCRep1JWH11c.wig: chromosome chr13 has 120284312 bases, but item ends at 120284500
line 3687123 of H3K4me1ESCRep1JWH11c.wig: chromosome chr17 has 95272651 bases, but item ends at 95272725
line 3801840 of H3K4me1ESCRep1JWH11c.wig: chromosome chr16 has 98319150 bases, but item ends at 98319250
line 3932880 of H3K4me1ESCRep1JWH11c.wig: chromosome chr19 has 61342430 bases, but item ends at 61342625
Unrecognized line 4038044 of H3K4me1ESCRep1JWH11c.wig: track visibility=dense name="1e-09_k4me1_D1R1_allButD4R1wce_enriched_regions"

I know I can insert the -clip parameter to avoid and skip those errors, but, where/what exactly should I insert it in the script?

Best regards and thank you for your time!

[Mensur Dlakic]

I think you may be missing </URGENT> at the very end to make the syntax correct.

[ATpoint]

I would rather find out why there is a discrepancy between the chromsizes and the wig file. You are sure it is mm9 and not mm10? The error indicates a problem and just ignoring it would probably be not so smart. In the worst case you are using the wrong reference genome.

[matteo.zoia]

mm9 it is correct yes

[Carlo Yague]

Hello matteo,

You've conveyed urgency in your post, which should be avoided. Biostars, like most open science forums, is powered by volunteers who offer their time and expertise by volition and not by obligation. So, we cannot guarantee you an answer within a time period. We respond quickly, especially to questions posted on weekdays in the day, but this cannot be guaranteed.

I have removed the term conveying urgency (caps lock and < URGENT> ) from the title of your post for the above reason. Thank you for understanding.

Answer 1

[seidel]

It is essential that you know why you have elements outside the dimensions of your chromosomes. Do not simply ignore this error. However, if you know there is a trivial explanation, you can place -clip as an argument to the wigToBigWig utility:

./wigToBigWig -clip H3K4me1ESCRep1JWH11c.wig mm9.chrom.sizes.txt myBigWig.bw

[matteo.zoia]

I tried but it doesn't work. I run then :

./bedClip -truncate H3K4me1ESCRep1JWH11c.wig mm9.chrom.sizes.txt myCLIPPEDFILE.wig
./wigToBigWig myCLIPPEDFILE.wig mm9.chrom.sizes.txt myBigWigFILE.bw

anyway it sort me out blank files, 0 bytes, what could be the issue?

[Carlo Yague]

Can you post a few lines of your original wig file and of the chrom size file ?

[seidel]

Does your wig file contain the track definition line? (the error above suggests it does, "track visibility=dense..."). If so, you should remove it (grep -v track in.wig > out.wig). Does your wig file contain any chromosome entries not found in your mm9 chrsize file?