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LElmen
@LElmen
I've tried both index_col and 'Geneid', ... it is maybe another problem alltogether.
Conall Sauvey
@csauvey
index_col didn't work for me until i included the skiprows first
mbaughn
@mbaughn
The assertion statement will also totally fail if your dataset is missing the last column like mine was… lol
LElmen
@LElmen
Because it doesn't understand that the second row can be a header I guess
I think most of my homework is a total fail, but I'll fight through what I can.
Conall Sauvey
@csauvey
^
LElmen
@LElmen
Thanx for the tips!
vwfu
@vwfu
@olgabot I completed exercise 6 last week, and just now noticed it's been modified, and my command has been moved up one cell I think... Do I need to redo the exercise? There's a new cell under Exercise 6 that just says: #MODIFIED ASSIGNMENT STATEMENT ABOVE
ecwheele
@ecwheele
@LElmen did you try including: comment='#' inside of pd.read_table()
LElmen
@LElmen
I think it was something else, I had to rerun the import pandas and those, restarted my login. This worked (see scrnshot)
Screen Shot 2016-02-16 at 9.50.33 PM.png
ecwheele
@ecwheele
Woo!!
LElmen
@LElmen
I learned some things about slicing and indexing in python trying to googleshoot the problem. :smile:
This forum has been great help!
ecwheele
@ecwheele
While sometimes incredibly frustrating... combing through the google responses is the best way to learn!
LElmen
@LElmen
Usually I end up learning something else than what I was looking for, but that sometimes comes in handy later on (oh, didn't I read that somewhere...)
Olga Botvinnik
@olgabot
@vwfu what changed?
vwfu
@vwfu
Screen Shot 2016-02-16 at 9.58.34 PM.png
Olga Botvinnik
@olgabot
Hmm was that after you merged changes?
vwfu
@vwfu
i think it moved my answer to the cell above exercise 6? not quite sure...
Olga Botvinnik
@olgabot
Put your answer directly below -that’s where the grading code is
vwfu
@vwfu
done! i'll resubmit the hw in that case
Olga Botvinnik
@olgabot
you don’t have to “resubmit"
if you git add+commit+push your changes, it’ll update the pull request
vwfu
@vwfu
oh yeah that's what i meant by 'resubmit' sorry terminology
Olga Botvinnik
@olgabot
ah got it
just making sure!
I didn’t want you making a new branch or somethign
vwfu
@vwfu
nope haha
thanks !
LElmen
@LElmen
For the FPKM calculation, where do we get the total number of reads sequenced? The defined reads = from the bam is the read counts of feature of interest, isn't it?
ecwheele
@ecwheele
Sum the values in the column of feature counts
Those are the total number of reads that mapped to genes. Each Fragment mapped to a gene comes from 1 read
So there are also sequencing reads that don't map to genes, but in this case we are not interested in them so we take the total sum of fragments (reads) that mapped to genes by summing that column in the featurecounts output
LElmen
@LElmen
what is the header of the feature counts output, I might be missing columns
mbaughn
@mbaughn
I was too
ecwheele
@ecwheele
it should be the last column that is labelled /home/ucsd-trainxx/projects/shalek2013/processed_data/S10.Aligned.out.sorted.bam
LElmen
@LElmen
No, I have it! Thank you both!
LElmen
@LElmen
I don't get it... If FPMK= "counts observed for feature x" (which is the sum of the /...//sorted.bam)/ length (summed up length column) * Total reads sequenced,
where are the total reads sequenced no?
ecwheele
@ecwheele
FPKM = ((counts to a gene / length of the gene) / total reads sequenced)* 1e9
total reads sequenced is the sum of the counts column
which you can get with:
reads = s10_featurecounts['/home/ucsd-trainxx/projects/shalek2013/processed_data/S10.Aligned.out.sorted.bam']
total counts = reads.sum()
LElmen
@LElmen
Finally got it... I've been trying to sum up ALL genes and counts here... (For once syntax wasn't the problem). I should probably not try to do any calculations ever after 10pm. If I take the example gene given in the assert it matches now. Thank you!!\
mbaughn
@mbaughn
If anyone is suspicious of their symbolic links, you can print their paths using the -H option of ls:
E.G.
[ucsd-train03@tscc-login1 scratch]$ ls -lhaH

lrwxrwxrwx   1 ucsd-train03 biom262-group   27 Feb  8 09:17 shalek2013 -> /home/ucsd-train03/projects
mbaughn
@mbaughn
also
tree -f
is like " ls methadone" for the GUI-addicted
I will never again just keep mashing cd… ls… cd… ls… to dive down into nested folders and figure out where things are
tree -f then copy paste the full path and cd there
ecpierce
@ecpierce
Has Oliviers homework been assigned/when is it due?
ericsan119
@ericsan119
Does anyone know how to install Varscan on TSCC?