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Running bigWigToWig using Anaconda in a Linux System

Hi,

I've been trying to convert a .bw file to a wig file using bigWigtoWig. When I run the command my error is:

Permission denied mustOpenFd: Can't open dm6.27way.phastCons.bw to read

The code I used:

bigWigToWig dm6.27way.phastCons.bw out.wig -chrom=chr3L

I've setup bigWigToWig by installing the package through anaconda and I have my virtual environment containing the package active in linux.

I presumed this is an issue with the files not having executing privileges, and I've trying using chmod +x on all the files I could think of. But still no luck.

anaconda bigwig
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written by jachimowicz9002 • jachimowicz9002

Are you running the program from the correct directory? Have you tried providing the full path to dm6.27way.phastCons.bw?

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written by dr_cfoster dr_cfoster

I tried running the full path, but I'm getting the same error. I'm actually not sure what the correct directory would be, but I did try placing it in my bin directory in my environment. I also tried placing it where the package is located.

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written by jachimowicz9002 • jachimowicz9002

1 answer

I managed to get it working without using anaconda.

This is what I had to do:

chmod 777 wigs/*

./bigWigToWig dm6.27way.phastCons.bw out.wig

In my wigs directory I have the bigWigToWig file and my input .bw file.

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written by jachimowicz9002 • jachimowicz9002

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