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BICF
Astrocyte
rnaseq
Commits
18c034ed
Commit
18c034ed
authored
Jun 25, 2018
by
Jonathan Gesell
Browse files
Corrected issue where a gene with 0 read counts could crash the dea.R scripts.
parent
2adff316
Pipeline
#2043
failed with stage
in 185 minutes and 52 seconds
Changes
3
Pipelines
1
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Inline
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nextflow.config
View file @
18c034ed
process
.
executor
=
'slurm'
process
.
queue
=
'128GB,256GB,256GBv1'
process
.
clusterOptions
=
'--hold'
trace
.
enabled
=
tru
e
trace
.
enabled
=
fals
e
trace
.
file
=
'pipeline_trace.txt'
trace
.
field
=
'task_id,native_id,process,name,status,exit,submit,start,complete,duration,realtime'
process_scripts
@
291e1c35
Compare
0bdf56d5
...
291e1c35
Subproject commit
0bdf56d5bdb9252ce418fcf7d0c7bdbcee9ff4a1
Subproject commit
291e1c352873ce14881ab8b1822fa7d3183b946b
workflow/scripts/dea.R
View file @
18c034ed
...
...
@@ -94,6 +94,7 @@ for (i in 1:a) {
filt.out
<-
na.omit
(
output
[
output
$
fdr
<
0.05
,])
if
(
nrow
(
filt.out
)
>
2
)
{
subset
<-
logcpm
[
row.names
(
logcpm
)
%in%
filt.out
$
symbol
,]
subset
<-
subset
[
!
apply
(
subset
,
1
,
function
(
x
)
{
any
(
x
==
0
)}),]
gnames
<-
filt.out
[
c
(
'ensembl'
,
'symbol'
)]
s
<-
merge
(
gnames
,
subset
,
by.x
=
"ensembl"
,
by.y
=
"row.names"
,
all.x
=
FALSE
,
all.y
=
TRUE
,
sort
=
FALSE
)
STREE
<-
hclust
(
dist
(
t
(
subset
)))
...
...
@@ -148,6 +149,7 @@ for (i in 1:a) {
filt.out
<-
na.omit
(
output
[
output
$
fdr
<
0.05
,])
if
(
nrow
(
filt.out
)
>
2
)
{
subset
<-
logcpm
[
row.names
(
logcpm
)
%in%
filt.out
$
symbol
,]
subset
<-
subset
[
!
apply
(
subset
,
1
,
function
(
x
)
{
any
(
x
==
0
)}),]
gnames
<-
filt.out
[
c
(
'ensembl'
,
'symbol'
)]
s
<-
merge
(
gnames
,
subset
,
by.x
=
"ensembl"
,
by.y
=
"row.names"
,
all.x
=
FALSE
,
all.y
=
TRUE
,
sort
=
FALSE
)
STREE
<-
hclust
(
dist
(
t
(
subset
)))
...
...
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