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biom262/biom262-2016

Code and notebooks for BIOM262

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Mar 24 2016 17:46

bmlewis-UCSD synchronize #107
Mar 15 2016 23:44

apryan opened #130
Mar 15 2016 10:59

anupriyatripathi opened #129
Mar 13 2016 21:14

andersonbrookee synchronize #76
Mar 13 2016 21:12

andersonbrookee synchronize #76
Mar 10 2016 05:10

olgabot on gh-pages

Travis build 368 pushed to Gith… (compare)
Mar 10 2016 05:10

olgabot on gh-pages

Travis build 367 pushed to Gith… (compare)
Mar 10 2016 05:09

bioh4x on master

Update index.jade (compare)
Mar 10 2016 05:08

bioh4x on master

Update index.jade (compare)
Mar 10 2016 05:05

bioh4x on master

adding new last lecture powerpo… (compare)
Mar 08 2016 17:35

olgabot on gh-pages

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Mar 08 2016 17:32

bioh4x on master

Update index.jade adding link … (compare)
Mar 08 2016 16:33

bioh4x on master

Update Network Basics.ipynb fi… (compare)
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Mar 08 2016 03:01

bioh4x on master

week10_mod1_updates (compare)
Mar 07 2016 00:05

ohsamboss opened #128
Mar 04 2016 22:24

olgabot on gh-pages

Travis build 360 pushed to Gith… (compare)
Mar 04 2016 22:22

bioh4x on master

pptx updates for week09 (compare)
Mar 04 2016 22:20

bioh4x on master

updating with powerpoints (compare)
Mar 03 2016 15:44

olgabot on gh-pages

Travis build 358 pushed to Gith… (compare)

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

:-)

LElmen

@LElmen

Can anyone give me a hint on how to slice off row 1 and get the index column set? I've tried various 'set_index', index_col = '0', print [1:46984

this is not supposed to be hard :-(

mbaughn

@mbaughn

skiprows=1

http://pandas.pydata.org/pandas-docs/stable/generated/pandas.read_table.html

index_col is the other one

you can just specify the name of the column in single quotes

or put the column number

both seem to work

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!