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BICF
Astrocyte
chipseq_analysis
Commits
b880088c
Commit
b880088c
authored
Jul 31, 2019
by
Jeremy Mathews
Browse files
Change Annotate Peaks to GTF file reference
parent
f6036083
Pipeline
#4578
failed with stages
in 697 minutes and 39 seconds
Changes
2
Pipelines
1
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CHANGELOG.md
View file @
b880088c
...
...
@@ -10,6 +10,7 @@ All notable changes to this project will be documented in this file.
-
Add PlotProfile Option
-
Add Python version to MultiQC
-
Add and Update tests
-
Use GTF files instead of TxDb and org libraries in Annotate Peaks
## [publish_1.0.6 ] - 2019-05-31
### Added
...
...
workflow/scripts/annotate_peaks.R
View file @
b880088c
...
...
@@ -6,17 +6,11 @@
#* --------------------------------------------------------------------------
#*
#Currently Human or Mouse
# Load libraries
library
(
"ChIPseeker"
)
# Currently mouse or human
library
(
"TxDb.Hsapiens.UCSC.hg19.knownGene"
)
library
(
"TxDb.Mmusculus.UCSC.mm10.knownGene"
)
library
(
"TxDb.Hsapiens.UCSC.hg38.knownGene"
)
library
(
"org.Hs.eg.db"
)
library
(
"org.Mm.eg.db"
)
library
(
GenomicFeatures
)
# Create parser object
args
<-
commandArgs
(
trailingOnly
=
TRUE
)
...
...
@@ -31,14 +25,14 @@ genome_assembly <- args[2]
# Load UCSC Known Genes
if
(
genome_assembly
==
'GRCh37'
)
{
txdb
<-
TxDb.Hsapiens.UCSC.hg19.knownGene
annodb
<-
'org.Hs.eg.db'
txdb
<-
makeTxDbFromGFF
(
"/project/shared/bicf_workflow_ref/human/GRCh37/gencode.v19.chr_patch_hapl_scaff.annotation.gtf"
)
sym
<-
read.table
(
"/project/shared/bicf_workflow_ref/human/GRCh37/genenames.txt"
,
header
=
T
,
sep
=
'\t'
)
[,
4
:
5
]
}
else
if
(
genome_assembly
==
'GRCm38'
)
{
txdb
<-
TxDb.Mmusculus.UCSC.mm10.knownGene
annodb
<-
'org.Mm.eg.db'
txdb
<-
makeTxDbFromGFF
(
"/project/shared/bicf_workflow_ref/mouse/GRCm38/gencode.vM20.annotation.gtf"
)
sym
<-
read.table
(
"/project/shared/bicf_workflow_ref/mouse/GRCm38/genenames.txt"
,
header
=
T
,
sep
=
'\t'
)
[,
4
:
5
]
}
else
if
(
genome_assembly
==
'GRCh38'
)
{
txdb
<-
TxDb.Hsapiens.UCSC.hg38.knownGene
annodb
<-
'org.Hs.eg.db'
txdb
<-
makeTxDbFromGFF
(
"/project/shared/bicf_workflow_ref/human/GRCh38/gencode.v25.chr_patch_hapl_scaff.annotation.gtf"
)
sym
<-
read.table
(
"/project/shared/bicf_workflow_ref/human/GRCh38/genenames.txt"
,
header
=
T
,
sep
=
'\t'
)
[,
4
:
5
]
}
# Output version of ChIPseeker
...
...
@@ -54,18 +48,18 @@ names(files) <- design$Condition
# Granges of files
peaks
<-
lapply
(
files
,
readPeakFile
,
as
=
"GRanges"
,
header
=
FALSE
)
peakAnnoList
<-
lapply
(
peaks
,
annotatePeak
,
TxDb
=
txdb
,
annoDb
=
annodb
,
tssRegion
=
c
(
-3000
,
3000
),
verbose
=
FALSE
)
peakAnnoList
<-
lapply
(
peaks
,
annotatePeak
,
TxDb
=
txdb
,
tssRegion
=
c
(
-3000
,
3000
),
verbose
=
FALSE
)
column_names
<-
c
(
"chr"
,
"start"
,
"end"
,
"width"
,
"strand_1"
,
"name"
,
"score"
,
"strand"
,
"signalValue"
,
"pValue"
,
"qValue"
,
"peak"
,
"annotation"
,
"geneChr"
,
"geneStart"
,
"geneEnd"
,
"geneLength"
,
"geneStrand"
,
"geneId"
,
"transcriptId"
,
"distanceToTSS"
,
"ENSEMBL"
,
"symbol"
,
"geneName"
)
"geneLength"
,
"geneStrand"
,
"geneId"
,
"transcriptId"
,
"distanceToTSS"
,
"symbol"
)
for
(
index
in
c
(
1
:
length
(
peakAnnoList
)))
{
filename
<-
paste
(
names
(
peaks
)[
index
],
".chipseeker_annotation.tsv"
,
sep
=
""
)
df
<-
as.data.frame
(
peakAnnoList
[[
index
]])
colnames
(
df
)
<-
column_names
write.table
(
df
[
,
!
(
names
(
df
)
%in%
c
(
'strand_1'
))],
filename
,
sep
=
"\t"
,
quote
=
F
,
row.names
=
F
)
df_final
<-
merge
(
df
,
sym
,
by.x
=
"geneId"
,
by.y
=
"ensembl"
,
all.x
=
T
)
colnames
(
df_final
)
<-
column_names
write.table
(
df_final
[
,
!
(
names
(
df_final
)
%in%
c
(
'strand_1'
))],
filename
,
sep
=
"\t"
,
quote
=
F
,
row.names
=
F
)
# Draw individual plots
...
...
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