BigWig2Bed.pl issue

[yuhongning]

Dear developer,
Your script is exactly what I am looking for to convert mappability bigwig file to bed file, however, when I tried to convert a downloaded bigwig file (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/), it errored out on each line "Argument .... isn't numeric in addition (or multiplication) ...". Does the expected input file a "bigwig" or other type of file?

Thanks,

yuhong ning

[CancerGenome]

Hi Yuhong,

I think bigwig file has a different format with wig file. The wig file here is generated by gem-2-wig.

See this command line:
gem-2-wig -I rn5.index.gem -i rn5_100.mappability -o rn5_100 # create wig file based on raw ASCII Score
./BigWig2Bed.pl rn5_100.wig | bgzip -c > rn5_100.wig.mapQ.gz # use inhouse tool, covert BigWig format to Bed and bgzip for tabix index.

[yuhongning]

Thanks, Yu. I also found a R package to do the conversion. Best regards, Yuhong

…

On Tue, Aug 15, 2017 at 6:37 PM, Wang Yu ***@***.***> wrote: Hi Yuhong, I think bigwig file has a different format with wig file. The wig file here is generated by gem-2-wig. See this command line: gem-2-wig -I rn5.index.gem -i rn5_100.mappability -o rn5_100 # create wig file based on raw ASCII Score ./BigWig2Bed.pl rn5_100.wig | bgzip -c > rn5_100.wig.mapQ.gz # use inhouse tool, covert BigWig format to Bed and bgzip for tabix index. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ARrNTS34d-RJVDzlLTJV2gVs2GLHH85Hks5sYkf2gaJpZM4MqdKp> .