Error with bdg2bw.

[Anupriya Verma]

Hello,

I am using bdg2bw for conversion of my bedGraph files to bigwig format. 

I ran this script : bdg2bw breast_cancer_histone_modification_SRR2044723_treat_pileup.bdg hg38.chrom.sizes.

And got following error:

Expecting number got -1 line 1 of stdin

needLargeMem: trying to allocate 0 bytes (limit: 100000000000)

However, if I run bedtools slop, I get such file:

20      0       -1      1.53917

20      55978   -1      1.54380

20      55997   -1      1.56040

20      56001   -1      1.57700

20      56010   -1      1.61020

20      56012   -1      1.62680

20      56019   -1      1.64340

20      56020   -1      1.66000

20      56021   -1      1.67660

20      56023   -1      1.69320

But when I run bedClip after this, it's throwing error: Expecting number got -1 line 1 of output_file_from_bedtoolslop.

How to solve this problem??

Thanks in advance.
 

[Tao Liu]

Hi Anupriya,

My guess is that the chromosome names in bdg file are like ‘1, 2, 3…’ but the names in 'hg38.chrom.sizes' are ‘chr1, chr2, chr3, …’.

Best,
Tao

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