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  • Mar 24 2016 17:46
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Youtong Huang
@smugunicorn
Screen Shot 2016-02-12 at 9.34.44 AM.png
Olga Botvinnik
@olgabot
okay see where it says “file not found"
Youtong Huang
@smugunicorn
yeah
Olga Botvinnik
@olgabot
that’s because in the script it says [S10 R1 fastq file] and [S10 R2 fastq file] which indicates that you need to replace that placeholder with the real file
the file names are in the s10_align.sh file
Youtong Huang
@smugunicorn
um... oh... wait LOL i got confused and just copy pasted your codes
Olga Botvinnik
@olgabot
side note - I’m surprised the username @smugunicorn has not been taken until now!
yeah you gotta read them!
Youtong Huang
@smugunicorn
hahah xD
Olga Botvinnik
@olgabot
remember: “copy-paste-think"
Youtong Huang
@smugunicorn
T^T yessss it worked... thanks so much @olgabot
Olga Botvinnik
@olgabot
yayy!!!!!!
“copy-paste-think” is a lot of programming/bioinformatics .. someone out there has a solution to something that’s slightly different so you have to think about what you need to change for yours
is the video call for today
so you can type git co[TAB] and it’ll autocomplete git commit
mbaughn
@mbaughn
Thank you!
LElmen
@LElmen
I can't find the instructions for how to I kill a specific job on tscc? I forgot to rename the jobs and some other details so I had to resubmit, but now I have several jobs running. I thought ctrlC killed all jobs, but they are still running?
ecwheele
@ecwheele
qdel jonid#
jobid#
LElmen
@LElmen
Thank you!
LElmen
@LElmen
ls
Olga Botvinnik
@olgabot
?
I can tell you what files I currently have
Alannah Miranda
@ahmirand
my s10_featurecounts.txt file has an extra column that is headed by the code i used to run the featurecounts job... and every time i get rid of said column the next few cells don't work/have an assertion error and when i leave the column in, i think the cells are still returning wrong answers. I've tried rerunning the job and compared it with the code that is in the notebook we worked on in class, but i can't figure out whats wrong. halp pls :disappointed_relieved:
Olga Botvinnik
@olgabot
can you show the code?
we can fix this
Alannah Miranda
@ahmirand
Screen Shot 2016-02-12 at 12.55.45 PM.png
here's the code from the notebook, but did you want to see what I used for to run the job too?
Olga Botvinnik
@olgabot
yeah that looks correct
where is the error coming from?
can you show the code and the error message?
Alannah Miranda
@ahmirand

well if I leave the column there, then the following cells seem to be working but the

sns.distplot(s10_featurecounts['/home/ucsd-train17/projects/shalek2013/processed_data/S10.Aligned.out.sorted.bam'])

results doesn't really look right to me, but then again I'm not sure what it should look like, but it looks like this:

Screen Shot 2016-02-12 at 12.56.02 PM.png

and when I use this to remove the last column:

s10_featurecounts = pd.read_table('s10_featureCounts.txt', skiprows=1, index_col=0, usecols= ['Chr', 'Start', 'End', 'Strand', 'Length'])

I get this error:

Olga Botvinnik
@olgabot
why doesn’t it look right to you>
and whih column are you removing?
remember that the example data is usign ucsd-train01
so every time you see ucsd-train01 you need to replace that with ucsd-train17
You NEED that big column because that’s the read counts!!
Alannah Miranda
@ahmirand
Screen Shot 2016-02-12 at 1.08.51 PM.png
Olga Botvinnik
@olgabot
that distribution is exactly what it should look like
So you need that column - don’t ignore it
it’s the read counts per gene
the distribution is exactly what it should be
it looks big and crazy because theres some genes that had 10000s of reads mapping to it
the KeyError is like a NameError except in teh dataframe
it can’t find a column named that