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Olga Botvinnik
@olgabot
check out the permissions: -rw-r—r—
the first - means not a folder
then the first trio of rw- is for the user, who is bmreilly and can read-write-execute
then the next trio is “group” (tscc-group in this case) and the last trio is “other” (i.e. everyone else)
someone has messed with your folder
we need to get them to fix it
LElmen
@LElmen
Does bmreilly have red hair by any chance? Because the person that helped me remove the softlink I created that looped back to the same place, deleted the whole thing - since it linked to itself
Olga Botvinnik
@olgabot
I don’t know
it’s brian reilley
I’m emailing them now
ecwheele
@ecwheele
yes he does
Olga Botvinnik
@olgabot
if they used their account then it messes up yours
LElmen
@LElmen
He then copied his stuff so that I could get the harismendy files and follow in class
Olga Botvinnik
@olgabot
they need to use YOUR account to do things in your home
yeah that’s what happened
LElmen
@LElmen
This is a total laugh or cry moment (mostly laugh though)
Olga Botvinnik
@olgabot
yeah
I just emailed
hopefully that’ll get fixed soon :(
sit tight until then
:pray:
LElmen
@LElmen
It all started with that I made that soft link that linked to itself haha
Olga Botvinnik
@olgabot
hah :)
it’s all part of the learning process
ecwheele
@ecwheele
If you can't laugh at all your ridiculous fails in science you will never make it out of grad school! :)
That's why PhD comics exist!
Olga Botvinnik
@olgabot
It’s true!
LElmen
@LElmen
As a matter of fact in this specific class, I learn much more by things NOT working, because otherwise I wouldn't think so much about what all flags etc mean.
Olga Botvinnik
@olgabot
:satisfied:
yep!
that’s the beauty of all this mess
bmlewis-UCSD
@bmlewis-UCSD
```del s13_kallisto['silly extra column i added ']
del s13_kallisto['silly extra column i added ']
bmlewis-UCSD
@bmlewis-UCSD
s10_featurecounts = pd.read_table('S*10_featureCounts.txt')
print(s10_featurecounts.shape)
s10_featurecounts.head()
S* is lowercase in the nb file, changed to cap S to get to run
Olga Botvinnik
@olgabot
Oh okay thanks!
bmlewis-UCSD
@bmlewis-UCSD
just sharing
bmlewis-UCSD
@bmlewis-UCSD
assert s10_featurecounts.shape == (46983, 6)
assert (s10_featurecounts.columns[:-1] == pd.Index(['Chr', 'Start', 'End', 'Strand', 'Length'],
      dtype='object')).all()

---------------------------------------------------------------------------
AssertionError                            Traceback (most recent call last)
<ipython-input-16-d862fc3ff3b3> in <module>()
----> 1 assert s10_featurecounts.shape == (46983, 6)
      2 assert (s10_featurecounts.columns[:-1] == pd.Index(['Chr', 'Start', 'End', 'Strand', 'Length'],
      3       dtype='object')).all()

AssertionError:
# my output (2993, 6)
s10_featurecounts = pd.read_table('S10_featureCounts.txt', index_col=0, header=1)
print(s10_featurecounts.shape)
s10_featurecounts.head()
is my S10_featurecounts.txt file messed up (too short) or I am messing up exercise 6
Olga Botvinnik
@olgabot
Can you show a screenshot of the first 5 lines of the data frame ie the head command?
The assertion error is if there are any mismatches in your file
Did you use chr11 or the full dataset?
For featurecounts?
bmlewis-UCSD
@bmlewis-UCSD
    Chr    Start    End    Strand    Length    /home/ucsd-train21/projects/shalek2013/processed_data/S10.Aligned.out.sorted.bam
Geneid                        
ENSMUSG00000082286.10    chr11;chr11;chr11;chr11;chr11;chr11    3125904;3127479;3128929;3129765;3130153;3130793    3126058;3127644;3129520;3129911;3130313;3131004    +;+;+;+;+;+    1433    204
ENSMUSG00000023764.18    chr11;chr11;chr11;chr11;chr11;chr11;chr11;chr1...    3131850;3132216;3132887;3133072;3134318;313462...    3132131;3132327;3132965;3133207;3134501;313473...    -;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;...    4432    0
ENSMUSG00000087111.1    chr11;chr11;chr11    3142048;3142594;3143180    3142111;3142669;3143363    +;+;+    324    0
ENSMUSG00000081208.1    chr11    3149742    3150955    -    1214    0
ENSMUSG00000020457.13    chr11;chr11;chr11;chr11;chr11;chr11;chr11;chr1...    3249907;3252160;3252644;3254512;3256543;325930...    3250365;3252282;3252811;3254642;3256712;325937...    -;-;-;-;-;-;-;-;-    1546    10030
want a screen shot instead?
Olga Botvinnik
@olgabot
Yeah it looks like you used chr11
It's my mistake because I thought it would take to long but featurecounts is really fast so use the full gtf file
bmlewis-UCSD
@bmlewis-UCSD
in the feature counts.sh file