wig to bigwig error

Question

[sneup]

Hi,

I was running:

./wigToBigWig CMML_5hmC.wig GRCh38_EBV.chrom.sizes CMML_5hmC.bigwig

I got this error:

Expecting double field 1 line 214451062 of CMML_5hmC.wig, got 0.58,21627712,21631370,22401293,22410.173685

Can you help solving this issue?

Answer 1

[Istvan Albert]

looks like the file is corrupted and contains information that is not in wiggle format

https://genome.ucsc.edu/goldenPath/help/wiggle.html

it should look like this (two columns)

variableStep chrom=chr2
300701 12.5
300702 12.5
300703 12.5

instead at line 214,451,062 you have:

0.58,21627712,21631370,22401293,22410.173685

[sneup]

Hi, Thank you for the insight. Is there any way I can edit that line?

[Istvan Albert]

if it is just one line you can delete say line 234 with

cat olddata.txt | sed 234d  > newdata.txt

if there are more lines then I would investigate a little more to figure out what is going on, then you can remove lines that have a certain type of pattern in them

[sneup]

Thank you.