diff --git a/seqspec_templates/10x_rna_atac.yaml b/seqspec_templates/10x_rna_atac.yaml index 601149c..0e98753 100644 --- a/seqspec_templates/10x_rna_atac.yaml +++ b/seqspec_templates/10x_rna_atac.yaml @@ -9,7 +9,7 @@ modalities: - rna - atac lib_struct: https://teichlab.github.io/scg_lib_structs/methods_html/10xChromium_multiome.html -library_protocol: Any +library_protocol: Custom library_kit: Illumina Truseq Dual Index sequence_protocol: Illumina NovaSeq 6000 sequence_kit: NovaSeq 6000 v1.5 @@ -23,7 +23,7 @@ library_spec: sequence_type: joined sequence: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNNNNNNNNNNNNXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXAGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG min_len: 153 - max_len: 250 + max_len: 1150 onlist: null regions: - !Region @@ -86,7 +86,7 @@ library_spec: sequence_type: random sequence: XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX min_len: 1 - max_len: 98 + max_len: 1000 onlist: null regions: null - !Region @@ -130,7 +130,7 @@ library_spec: sequence_type: joined sequence: AATGATACGGCGACCACCGAGATCTACACNNNNNNNNNNNNNNNNCGCGTCTGTCGTCGGCAGCGTCAGATGTGTATAAGAGACAGXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXCTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG min_len: 153 - max_len: 250 + max_len: 1150 onlist: null regions: - !Region @@ -193,7 +193,7 @@ library_spec: sequence_type: random sequence: XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX min_len: 1 - max_len: 98 + max_len: 1000 onlist: null regions: null - !Region diff --git a/seqspec_templates/generic_atac.yaml b/seqspec_templates/generic_atac.yaml new file mode 100644 index 0000000..d2716a7 --- /dev/null +++ b/seqspec_templates/generic_atac.yaml @@ -0,0 +1,93 @@ +!Assay +seqspec_version: 0.3.0 +assay_id: generic_atac +name: generic ATAC +doi: Not-Specified +date: 15 September 2020 +description: Generic ATAC-seq +modalities: +- atac +lib_struct: Not-Specified +library_protocol: single-cell ATAC-seq (OBI:0002764) +library_kit: Not-Specified +sequence_protocol: Custom +sequence_kit: Custom +sequence_spec: [] +library_spec: +- !Region + parent_id: null + region_id: atac + region_type: atac + name: ATAC + sequence_type: joined + sequence: AATGATACGGCGACCACCGAGATCTACACGCGATCGAGGACGGCAGATGTGTATAAGAGACAGXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXCACCGTCTCCGCCTCAGATGTGTATAAGAGACAGXXXXXXXXXXXXXXXXATCTCGTATGCCGTCTTCTGCTTG + min_len: 153 + max_len: 1150 + onlist: null + regions: + - !Region + parent_id: atac + region_id: atac-illumina_p5 + region_type: illumina_p5 + name: Illumina P5 + sequence_type: fixed + sequence: AATGATACGGCGACCACCGAGATCTACAC + min_len: 29 + max_len: 29 + onlist: null + regions: null + - !Region + parent_id: atac + region_id: atac-read1 + region_type: custom_primer + name: read 1 + sequence_type: fixed + sequence: GCGATCGAGGACGGCAGATGTGTATAAGAGACAG + min_len: 34 + max_len: 34 + onlist: null + regions: null + - !Region + parent_id: atac + region_id: gDNA + region_type: gdna + name: gDNA + sequence_type: random + sequence: XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX + min_len: 1 + max_len: 1000 + onlist: null + regions: null + - !Region + parent_id: atac + region_id: atac-read2 + region_type: custom_primer + name: read 2 + sequence_type: fixed + sequence: CACCGTCTCCGCCTCAGATGTGTATAAGAGACAG + min_len: 34 + max_len: 34 + onlist: null + regions: null + - !Region + parent_id: atac + region_id: atac-cell_barcode + region_type: barcode + name: R2 Cell Barcode + sequence_type: random + sequence: XXXXXXXXXXXXXXXXXXXXXX + min_len: 22 + max_len: 22 + onlist: null + regions: null + - !Region + parent_id: atac + region_id: atac-illumina_p7 + region_type: illumina_p7 + name: Illumina P7 + sequence_type: fixed + sequence: ATCTCGTATGCCGTCTTCTGCTTG + min_len: 24 + max_len: 24 + onlist: null + regions: null \ No newline at end of file