diff --git a/example/input/config.yaml b/example/input/config.yaml index b5289ff3cd568dace15eeb7ea6f0f4051baf7e70..afd9bf1edfd628e7117768c6fce241a0dd4088f2 100644 --- a/example/input/config.yaml +++ b/example/input/config.yaml @@ -76,6 +76,7 @@ samples: # STRING. "ATACseq" or "ChIPseq". Only data type specific steps are executed. Currently, if set to ChIP-Seq, ATAC-seq specific steps like RSS adjustment are not executed, and peak calling may include control samples if the sample table specifies this. dataType: "ChIPseq" + dataType: "ATACseq" ########################### # SECTION additionalInput # @@ -178,7 +179,7 @@ postalign: ####################### # NOTE: There is usually no need to modify the parameters here. - +scripts: # INTEGER. Default 4000. The region size in bp that specifies what is considered within a TSS. The STATS script does a TSS enrichment test to test whether or not ATAC-Seq reads are primarily located within annotated TSS as opposed to outside of TSS regions. A value of 4000 means the region from -2kb up to +2kb of annotated TSS. STATS_script_withinThr: 4000 diff --git a/example/templates/hg19/config.yaml b/example/templates/hg19/config.yaml index 84ae06585973d423dee6dead42113fde5dadf3ee..798589b3c90f626be24f681bfc076a3e73c93291 100644 --- a/example/templates/hg19/config.yaml +++ b/example/templates/hg19/config.yaml @@ -178,7 +178,7 @@ postalign: ####################### # NOTE: There is usually no need to modify the parameters here. - +scripts: # INTEGER. Default 4000. The region size in bp that specifies what is considered within a TSS. The STATS script does a TSS enrichment test to test whether or not ATAC-Seq reads are primarily located within annotated TSS as opposed to outside of TSS regions. A value of 4000 means the region from -2kb up to +2kb of annotated TSS. STATS_script_withinThr: 4000 diff --git a/example/templates/hg38/config.yaml b/example/templates/hg38/config.yaml index 528ffe1b67cfb6bf574af3c215802364ad98ece2..3db02ee01b86a920f2e2ac89722833721697e0b8 100644 --- a/example/templates/hg38/config.yaml +++ b/example/templates/hg38/config.yaml @@ -178,7 +178,7 @@ postalign: ####################### # NOTE: There is usually no need to modify the parameters here. - +scripts: # INTEGER. Default 4000. The region size in bp that specifies what is considered within a TSS. The STATS script does a TSS enrichment test to test whether or not ATAC-Seq reads are primarily located within annotated TSS as opposed to outside of TSS regions. A value of 4000 means the region from -2kb up to +2kb of annotated TSS. STATS_script_withinThr: 4000 diff --git a/example/templates/mm10/config.yaml b/example/templates/mm10/config.yaml index 1f5eaca24e3565cdc0738fc8feeed0726d5c08e5..ea117b6a7e84a7fc911f6c2322055d61b1768cf0 100644 --- a/example/templates/mm10/config.yaml +++ b/example/templates/mm10/config.yaml @@ -173,8 +173,9 @@ postalign: # SECTION scripts # ####################### -# NOTE: There is usually no need to modify the parameters here. - + # NOTE: There is usually no need to modify the parameters here. +scripts: + # INTEGER. Default 4000. The region size in bp that specifies what is considered within a TSS. The STATS script does a TSS enrichment test to test whether or not ATAC-Seq reads are primarily located within annotated TSS as opposed to outside of TSS regions. A value of 4000 means the region from -2kb up to +2kb of annotated TSS. STATS_script_withinThr: 4000