Question: Sorting RNA-seq data
0
gravatar for agrisimo2
6 weeks ago by
agrisimo20
agrisimo20 wrote:

Hello,

I have some RNA-seq data on an Excel spreadsheet. My gene/s of interest follow a particular expression pattern. I would like to know if it is possible to sort the data/identify genes that match 3 conditions set by me. For example, I'd like to be able to see all the genes that match this expression pattern :

Cell line A < Cell Line B < Cell line C > Cell line D
rna-seq • 175 views
ADD COMMENTlink modified 6 weeks ago by zx87545.6k • written 6 weeks ago by agrisimo20

Please provide example input and expected output.

ADD REPLYlink written 6 weeks ago by zx87545.6k

For example-

           Cell A         Cell B       Cell C     Cell D
Gene A    0.115175459   3.484635909 6.571842857 4.349035833
Gene B    0.021664012   2.939972182 3.448264286 3.8535915
Gene C    0.014484529   3.347903818 5.250840143 4.148886458
Gene D    0.0749899     33.82436091 52.07118571 30.74083333

The command should exclude gene B from the data set, since it does not follow the pattern A < B < C > D, and provide me with a list of genes that does so Gene A,C and D.

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by agrisimo20
1

I have some RNA-seq data on an Excel spreadsheet.

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ADD REPLYlink written 6 weeks ago by Pierre Lindenbaum114k
2
gravatar for EagleEye
6 weeks ago by
EagleEye5.9k
Sweden
EagleEye5.9k wrote:

If you are using Microsoft Excel,

=IF(AND(A1<B1,B1<C1,C1>D1),"YES","NO")
ADD COMMENTlink modified 6 weeks ago by zx87545.6k • written 6 weeks ago by EagleEye5.9k
2
gravatar for Pierre Lindenbaum
6 weeks ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum114k wrote:

With awk that would be:

awk '($2 < $3 && $3 < $4 && $4>$5 )'
ADD COMMENTlink modified 6 weeks ago by zx87545.6k • written 6 weeks ago by Pierre Lindenbaum114k
1
gravatar for zx8754
6 weeks ago by
zx87545.6k
London
zx87545.6k wrote:

Using R:

# read the file, something like:
df1 <- read.table("myFile.txt")

# then filter
df1[ df1$CellA < df1$CellB & df1$CellB < df1$CellC & df1$CellC > df1$CellD, ]
ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by zx87545.6k
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