convert *.bdg file to *.bw file

Question

[yueli7]

Hello,

I tried to convert *.bdg file to *.bw file.

I have bedClip software in the folder.

Thanks in advance for any help!

Best,

Yue

administrator@ACB:~/bedtools2-2.26.0$ sh bdg2bw.sh flag1_FE.bdg hg38.len
bdg2bw.sh: 19: bdg2bw.sh: bedClip: not found
/usr/bin/bedtools
sort: cannot read: flag1_FE.bdg.clip: No such file or directory
bdg2bw.sh: 23: bdg2bw.sh: Bad substitution

Answer 1

[Ram]

You need to have software on $PATH, not in the current working folder. You seem to be running into this error a lot. Follow the same procedure I gave you earlier, but with the path to bedClip and bedtools

[yueli7]

Hello, RamRs

Thank you so much for your great help!

I have all the file in my folder.

Thank you again!

Best,

Yue Li

administrator@ACB-HuangLab-Ubuntu:~/bedtools2-2.26.0/bin$ ./bedClip
bedClip - Remove lines from bed file that refer to off-chromosome locations.
usage:
bedClip [options] input.bed chrom.sizes output.bed
chrom.sizes is a two-column file/URL: <chromosome name=""> <size in="" bases="">
If the assembly <db> is hosted by UCSC, chrom.sizes can be a URL like
http://hgdownload.soe.ucsc.edu/goldenPath/<db>/bigZips/<db>.chrom.sizes
or you may use the script fetchChromSizes to download the chrom.sizes file.
If not hosted by UCSC, a chrom.sizes file can be generated by running
twoBitInfo on the assembly .2bit file.
options:
-truncate  - truncate items that span ends of chrom instead of the
            default of dropping the items
-verbose=2 - set to get list of lines clipped and why
administrator@ACB-HuangLab-Ubuntu:~/bedtools2-2.26.0/bin$ sh bdg2bw.sh
Need 2 parameters! <bedgraph> <chrom info="">
/usr/bin/bedtools
administrator@ACB-HuangLab-Ubuntu:~/bedtools2-2.26.0/bin$ sh bdg2bw.sh    flag1_FE.bdg hg38.len
bdg2bw.sh: 19: bdg2bw.sh: bedClip: not found
/usr/bin/bedtools
bdg2bw.sh: 21: bdg2bw.sh: cannot create flag1_FE.bdg.sort.clip: Permission denied
bdg2bw.sh: 23: bdg2bw.sh: Bad substitution

[Ram]

What is the output to:

which -a bedClip
which -a bedtools

If either of those gives you an error, you need to add the location of those binaries to your $PATH. Computers cannot see what you see, so just because the executable in your directory, you shell won't recognize them.

[yueli7]

Hello, RamRs,

Thank you so much for your great help!

Thank you again!

Best,

Yue

administrator@ACB-HuangLab-Ubuntu:~/bedtools2-2.26.0/bin$ PATH=$PATH:~/bedtools2-2.26.0/bin sh bdg2bw.sh flag1_FE.bdg chromInfo.txt

[Ram]

Also, don't use sh to execute shell scripts unless you're sure the script is POSIX compliant. Use either . or bash. Certain features (such as process substitution) will not work when executed with sh.

[yueli7]

Hello, RamRs,

Thank you so much for your remaining.

It finally work!

Thank you again!

Best,

Yue li

administrator@Ab-Ubuntu:~/bedtools2-2.26.0/bin$ PATH=$PATH:~/bedtools2-2.26.0/bin ./bdg2bw.sh xaf.txt chromInfo.txt