Closed ssshell closed 8 years ago
portah
commented
8 years ago Have you compiled the repository? What actual error do you get?
PS. you can try CWL, https://github.com/common-workflow-language/workflows/blob/master/tools/bedtools-genomecov.cwl - I wrapped the latest version there
ssshell
commented
8 years ago Scarlet S. Shell, PhD Assistant Professor Department of Biology and Biotechnology Worcester Polytechnic Institute Life Sciences and Bioengineering Center 60 Prescott Street Room 4034 Worcester, MA 01605 508-831-5917 (office) 858-405-3650 (cell)
From: Andrey Kartashov notifications@github.com<mailto:notifications@github.com> Reply-To: arq5x/bedtools2 reply@reply.github.com<mailto:reply@reply.github.com> Date: Monday, May 2, 2016 at 11:43 AM To: arq5x/bedtools2 bedtools2@noreply.github.com<mailto:bedtools2@noreply.github.com> Cc: Scarlet Shell sshell@wpi.edu<mailto:sshell@wpi.edu>, Author author@noreply.github.com<mailto:author@noreply.github.com> Subject: Re: [arq5x/bedtools2] -pc (#398)
Have you compiled the repository? What actual error do you get?
PS. you can try CWL, https://github.com/common-workflow-language/workflows/blob/master/tools/bedtools-genomecov.cwl - I wrapped the latest version there
� You are receiving this because you authored the thread. Reply to this email directly or view it on GitHubhttps://github.com/arq5x/bedtools2/issues/398#issuecomment-216272354
I would like to use the –pc option with bedtools genomecov and I understand that while it is not in the release version, I should be able to use it by cloning the repository. I'm still getting an error message, perhaps because I'm not cloning the repository correctly. I cloned it by entering this into the command line:
git clone https://github.com/arq5x/bedtools2.git
And then I tried this command:
bedtools genomecov -d -pc -scale 1.25 -ibam noHP_1_expr_sorted.bam -g NC_008596.chrom.sizes > noHP_1_expr_sorted.coverage
If anyone can tell me what I'm doing wrong I would greatly appreciate it.