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Olga Botvinnik
@olgabot
that command is looking for a variable called s10_featurecounts
oh you figured it out got it..
@vwfu can you show the full code that’s producing the error?
vwfu
@vwfu

@olgabot featurecounts_s10_specific_genes = featurecounts_s10_specific_genes.copy()
featurecounts_s13_specific_genes = featurecounts_s13_specific_genes.copy()

featurecounts_s10_specific_genes.index.map(lambda x: x.split('.')0)
featurecounts_s13_specific_genes.index.map(lambda x: x.split('.')0)

featurecounts_s10_specific_genes_ensembl = featurecounts_s10_specific_genes.index.map(lambda x: x.split('.')0)
featurecounts_s13_specific_genes_ensembl = featurecounts_s13_specific_genes.index.map(lambda x: x.split('.')0)

featurecounts_s13_specific_genes_ensembl.head()

Olga Botvinnik
@olgabot
You need to add the pd.Series() code around it
Only DataFrames and Series can do.head()
I believe earlier it says to do:
pd.Series(featurecounts_s13_specific_genes.index.map(lambda x: x.split(‘.')[0]))
ack
ugh it formatted the quotes
those are supposed to be quotes
ericsan119
@ericsan119
@olgabot Yes I did...
Screen Shot 2016-02-15 at 3.00.51 PM.png
Olga Botvinnik
@olgabot
@ericsan119 was your TPM calculation correct?
did you have errors there?
someone ran into a problem where their TPM calculation was off in the 12th significant figure or something
Olga Botvinnik
@olgabot
if you’re getting errors that far into the value, don’t worry about it - I will acount for it
ericsan119
@ericsan119
@olgabot I check my calculation again, I didn't errors in exercise 8. So I think my TPM calculation is correct.
Olga Botvinnik
@olgabot
hmm the only thing I can think of is if you ddin’t add one
ericsan119
@ericsan119
Screen Shot 2016-02-15 at 3.24.19 PM.png
Olga Botvinnik
@olgabot
Yeah I’m checking with my answer now
Yeah what you have is correct - since the difference is in the .000000001 range I’ll adjust to ignore it
ericsan119
@ericsan119
Thank you @olgabot
thewilmergency
@thewilmergency
Hi I don't think my S13_featurecounts file is right because my exercise 13 output table doesn't have the row mentioned in the assertion cell
Screenshot 2016-02-15 18.07.34.png
I'm trying to figure out where in the process I didn't get the right file. Here are my S13-relevant files
Screenshot 2016-02-15 18.09.28.png
thewilmergency
@thewilmergency
Actually I might be okay.
Olga Botvinnik
@olgabot
Was it a gtf issue?
thewilmergency
@thewilmergency
what do you mean gtf issue?
Olga Botvinnik
@olgabot
How did you fix it?
thewilmergency
@thewilmergency
It's just that I thought my output was wrong bc I didn't see the assertion item in my first 5 rows
But then when I did .loc for the assert statement, I found it
I found a near match to the assertion statement.
Olga Botvinnik
@olgabot
Ah got it
thewilmergency
@thewilmergency
For many of my cells I'm just a little off in my final decimal spaces
Olga Botvinnik
@olgabot
Yeah that's fine
Other people have had that problem
LElmen
@LElmen
Hi Olga, I still have an output issue. I reran my s13_kallisto.sh script, but I get nothing in the processed data folder.
Screen Shot 2016-02-15 at 8.57.32 PM.png
Now I can't access the sh.err either
oups forgot to write nano
LElmen
@LElmen
It's this very long error message again
Screen Shot 2016-02-15 at 9.03.33 PM.png
LElmen
@LElmen
@olgabot Pls ignore... not sure what I've done but it works now.
Olga Botvinnik
@olgabot
Yay!
@LElmen when you figure out something like the ssh-add thing, that's a really useful thing to put in your cheatsheets
LElmen
@LElmen
Already done
:-)