/calculate-depth-and-breadth-of-coverage-from-a-bam-file/?utterances=da4199376189e72dba16d0784eCB%2FzCOvx%2B4NVrj5NRgELJEXPFMrWZceHKbd6HSSu7aIUZ%2BK64RlCBe%2FAiIY7GkZ%2BN9QApDbZ6CYGp9y%2B84fGEYQX%2BEZqaLFZFshltneu5PyivVJ0F50ccddrY%3D

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/calculate-depth-and-breadth-of-coverage-from-a-bam-file/?utterances=da4199376189e72dba16d0784eCB%2FzCOvx%2B4NVrj5NRgELJEXPFMrWZceHKbd6HSSu7aIUZ%2BK64RlCBe%2FAiIY7GkZ%2BN9QApDbZ6CYGp9y%2B84fGEYQX%2BEZqaLFZFshltneu5PyivVJ0F50ccddrY%3D

utterances-bot opened this issue 4 years ago · comments

Calculate Depth and Breadth of Coverage From a bam File - Daniel E. Cook

https://www.danielecook.com/calculate-depth-and-breadth-of-coverage-from-a-bam-file/

sjfleck · Answer 1 · Thu Dec 10 2020 11:01:22 GMT+0800 (China Standard Time)

Hello Daniel,
I wanted to try out your script, but I'm having a difficult time getting it working. My python has os, re, and subprocess, so I don't think that's the issue. I also have samtools loaded. Would you give an example of how to run this? What do you mean by "feed the function coverage a bam file"? Thank you in advance,
Steve

Daniel E Cook · Answer 2 · Tue Dec 15 2020 04:47:25 GMT+0800 (China Standard Time)

Steve - give mosdepth a try. It's going to be much faster for you and easier to work with.

sjfleck · Answer 3 · Fri Dec 18 2020 01:23:29 GMT+0800 (China Standard Time)

Daniel, thank you for the recommendation! I will check it out -Steve

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On Mon, Dec 14, 2020 at 3:47 PM Daniel E Cook ***@***.***> wrote: Steve - give mosdepth <http://www.github.com/brentp/mosdepth> a try. It's going to be much faster for you and easier to work with. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#8 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AMXPLMQOHWAIYGTECQVK7YTSUZ2WZANCNFSM4UUMJO3Q> .