Empty bigwig files after ucsc-bedGraphtobigwig

Question

[Katara]

I am trying to convert my BED files from SEACR peak calling to bedgraph and from bedgraph to bigwig, but I keep producing empty bigwig files.

My BED files are formatted as follows:

NC_035107.1 310306832 310307343 10.9568 0.0694997 NC_035107.1:310307047-310307061 NC_035107.1 310351194 310351867 15.4501 0.0815866 NC_035107.1:310351716-310351719 NC_035107.1 310423838 310424140 14.2837 0.0755432 NC_035107.1:310423946-310424060 NC_035108.1 140383 140875 9.82666 0.0755432 NC_035108.1:140605-140607 NC_035108.1 300836 301546 6.90464 0.0302173 NC_035108.1:301165-301176 NC_035108.1 311967 312556 19.2877 0.0876301 NC_035108.1:312201-312231 NC_035108.1 338912 339318 11.0202 0.0755432 NC_035108.1:339035-339045

I converted from BED to bedgraph using awk '{printf "%s\t%d\t%d\t%2.3f\n" , $1,$2,$3,$4}' BED.file > bedgraph.file as suggested from Converstion of BED with scores into bigWig

which made a bedgraph file containing the chromosome, start, stop, and signal (columns 1-4), but when I use

bedGraphToBigWig bedgraph.file Mychrom.sizes > bigwig.file

I am producing empty bigwig files and no error is returned. I cannot figure out what is preventing my files from being converted. I have tried changing the chromosome names to chr#, as suggested in a previous post, but still have the issue.

Any suggestions would be greatly appreciated!

Answer 1

[ATpoint]

Remove > from the command. It does not write to stdout but to the file on position three.

[Katara]

Thank you!!