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Core NGS Tools - Shared screen with speaker view
John Ludes-Meyers
01:28:03
yep
Josh Everson
01:29:22
https://wikis.utexas.edu/display/CoreNGSTools/Running+batch+jobs+at+TACC
Audrey Kelly
01:30:36
Sorry! Labmate was just asking what I was doing and I didn't realize I was on mute!
Audrey Kelly
01:30:41
*wasn't
John Ludes-Meyers
01:42:25
How can we look at everything in biocontainers?
Rachael Cox
01:43:26
John -- 'module avail' is the command you'd want for that
John Ludes-Meyers
01:45:56
Thanks
Rachael Cox
01:57:49
Taking Nazan, Elsy, and Miles to a breakout room! Text if you need anything Anna
John Ludes-Meyers
02:07:06
yes. Ran great!
John Ludes-Meyers
02:07:46
Sounds good!
Runhua Han
02:33:46
Are only of those reads that pass the QC shown here as N? What about those failed?
Rachael Cox
02:34:28
those that failed will have a 'Y' instead!
Runhua Han
02:34:35
Thanks!
Luke Hebert
02:35:53
I've seen ~ as a quality score which I understand is good, but it doesn't seem to be on this list
Luke Hebert
02:36:04
Are there different strings to translate quality score?
Rachael Cox
02:38:57
I think the '~' translates to the highest score possible, I don't Anna actually showed the full scale
Rachael Cox
02:39:14
The full thing is like!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
Emmanuel Bredu Asiedu
02:39:32
Do we get access to these slides? I think I missed part of the first lecture and would love to have it since the some part wasn't recorded.
Luke Hebert
02:39:35
Oh gotcha. That would make sense and I'm sure I could look that up later to make sure there aren't different strings. Thank you!
Luke Hebert
02:39:57
https://wikis.utexas.edu/display/CoreNGSTools
Luke Hebert
02:42:28
Or the X-Men are real
Josh Everson
02:42:38
ha!
Emmanuel Bredu Asiedu
02:42:50
Why should only the 3' ends be trimmed? Sorry if I missed that
Emmanuel Bredu Asiedu
02:45:28
Makes a lot of sense now. thanks
Runhua Han
03:04:49
How do I go back to my path? Ctrl C didn’t work
Runhua Han
03:05:02
Cool
Runhua Han
03:05:04
Thanks
Runhua Han
03:05:29
Got it. Thanks.
Luke Hebert
03:14:06
"cat small.sq | tail -n 20" didn't give me a numbered list for some reason. I also tried "tail -n 20 small.sq | cat"
Luke Hebert
03:14:17
(just gave me a regular tail list)
Rachael Cox
03:14:27
Gotta put the '-n' next to cat!
Rachael Cox
03:14:40
so 'cat -n small.fq | tail'
Luke Hebert
03:14:49
right! Thanks
Luke Hebert
03:24:06
1000/4
Juyeon Park
03:35:00
What does “%f.2\n” mean? seems like I missed this
Rachael Cox
03:37:02
%f asks awk to print in floating point notation, \n is saying put it on a new line
Rachael Cox
03:37:10
I think
Rachael Cox
03:37:37
I'm an awk amateur
John Ludes-Meyers
03:39:07
Ok. Thanks!
Brian Stokes
03:39:10
Thank you!
Luke Hebert
03:40:54
75 mins
Luke Hebert
03:41:47
I gotta take off, but thanks Anna!
Runhua Han
03:42:39
Leaving now. Thanks!
Christina Ortega
03:45:03
I have to leave for work but thank you for the lesson.