Skip to content

Commit

Permalink
update to fix snakemake
Browse files Browse the repository at this point in the history
  • Loading branch information
@hermanzhaozzzz
hermanzhaozzzz committed Jul 27, 2022
1 parent 0d6cb22 commit a271f4d
Show file tree
Hide file tree
Showing 5 changed files with 295 additions and 48 deletions.
5 changes: 4 additions & 1 deletion README.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,14 +6,17 @@
---
## 环境
```shell
conda install python r-base bowtie2 samtools iced r-ggplot2 r-rcolorbrewer
conda install python r-base bowtie2 samtools iced r-ggplot2 r-rcolorbrewer
conda install -c bioconda java-jdk hicexplorer

# 我用的版本
# python=3.9.13
# R=4.0.5
# bowtie2=2.4.5
# samtools=1.15.1
# iced=0.5.10
# java-jdk=1.8 # java openjdk version "1.8.0_312"
# hicexplorer=3.7.2
```

## 用法
Expand Down
2 changes: 1 addition & 1 deletion __back_info/step02_convert_abs_matrix_to_h5.ipynb
View file
Original file line number Diff line number Diff line change
Expand Up @@ -691,7 +691,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.7"
"version": "3.9.13"
}
},
"nbformat": 4,
Expand Down
2 changes: 1 addition & 1 deletion samples.json
View file
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"seq_mode": "PE", "samples": ["Hi-C_auxin-2days_rep1", "Hi-C_auxin-2days_rep2", "Hi-C_untreated_rep1", "Hi-C_untreated_rep2", "Hi-C_washoff-2days_rep1", "Hi-C_washoff-2days_rep2", "SRR400264_00", "SRR400264_01"], "thread": 20, "bowtie2_index": "/lustre1/chengqiyi_pkuhpc/zhaohn/1.database/db_genomes/genome_fa/genome_ucsc_mm39/genome_ucsc_mm39.fa.bowtie2_index", "bowtie2_params_global": "--very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder", "bowtie2_params_local": "--very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end --reorder", "ligation_site": "AAGCTAGCTT", "sort_ram_per_thread": "", "min_mapq": 10, "bin_sizes": [1000, 2000, 5000, 10000, 20000, 50000, 100000, 200000, 500000, 1000000, 10000000, 50000000, 100000000], "chr_sizes": "program/HiC-Pro_3.1.0/annotation/chrom_mm39.sizes", "digest_bed": "program/HiC-Pro_3.1.0/annotation/HindIII_resfrag_mm39.bed"}
{"seq_mode": "PE", "samples": ["Hi-C_auxin-2days_rep1", "Hi-C_auxin-2days_rep2", "Hi-C_untreated_rep1", "Hi-C_untreated_rep2", "Hi-C_washoff-2days_rep1", "Hi-C_washoff-2days_rep2", "SRR400264_00", "SRR400264_01"], "thread": 20, "bowtie2_index": "/lustre1/chengqiyi_pkuhpc/zhaohn/1.database/db_genomes/genome_fa/genome_ucsc_mm39/genome_ucsc_mm39.fa.bowtie2_index", "bowtie2_params_global": "--very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder", "bowtie2_params_local": "--very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end --reorder", "ligation_site": "AAGCTAGCTT", "sort_ram_per_thread": "", "min_mapq": 10, "bin_sizes": [1000, 2000, 5000, 10000, 20000, 50000, 100000, 200000, 500000, 1000000, 10000000, 50000000, 100000000], "chr_sizes": "program/HiC-Pro_3.1.0/annotation/chrom_mm39.sizes", "digest_bed": "program/HiC-Pro_3.1.0/annotation/HindIII_resfrag_mm39.bed", "restriction_sequence": "AAGCTT", "dangling_sequence": "AGCT"}
88 changes: 51 additions & 37 deletions step01_generate_samples.ipynb
View file
Original file line number Diff line number Diff line change
Expand Up @@ -142,15 +142,15 @@
},
{
"cell_type": "code",
"execution_count": 13,
"execution_count": 24,
"id": "23c456fe-e340-47f8-b543-a3fd1d2e7137",
"metadata": {
"execution": {
"iopub.execute_input": "2022-07-27T13:47:38.358557Z",
"iopub.status.busy": "2022-07-27T13:47:38.357927Z",
"iopub.status.idle": "2022-07-27T13:47:38.366402Z",
"shell.execute_reply": "2022-07-27T13:47:38.364410Z",
"shell.execute_reply.started": "2022-07-27T13:47:38.358496Z"
"iopub.execute_input": "2022-07-27T16:42:01.949424Z",
"iopub.status.busy": "2022-07-27T16:42:01.948705Z",
"iopub.status.idle": "2022-07-27T16:42:01.958672Z",
"shell.execute_reply": "2022-07-27T16:42:01.956959Z",
"shell.execute_reply.started": "2022-07-27T16:42:01.949360Z"
},
"tags": []
},
Expand All @@ -162,7 +162,17 @@
"# 酶的序列，例如：\n",
"# HindIII，为AAGCTAGCTT\n",
"# MboI，为GATCGATC\n",
"ligation_site = \"AAGCTAGCTT\""
"ligation_site = \"AAGCTAGCTT\"\n",
"\n",
"# for hicexplorer\n",
"# For example, for HindIII the\n",
"# restriction site is AAGCTT and the dangling end is\n",
"# AGCT. For DpnII, the restriction site and dangling end\n",
"# sequence are the same: GATC. This information is\n",
"# easily found on the description of the restriction\n",
"# enzyme.\n",
"restriction_sequence = \"AAGCTT\" # HindIII\n",
"dangling_sequence = \"AGCT\" # HindIII"
]
},
{
Expand Down Expand Up @@ -317,44 +327,44 @@
},
{
"cell_type": "code",
"execution_count": 18,
"execution_count": 31,
"id": "9f8bc7e0-52ec-4e76-828c-e3a18f0987c8",
"metadata": {
"execution": {
"iopub.execute_input": "2022-07-27T13:47:40.888779Z",
"iopub.status.busy": "2022-07-27T13:47:40.888070Z",
"iopub.status.idle": "2022-07-27T13:47:40.896037Z",
"shell.execute_reply": "2022-07-27T13:47:40.894297Z",
"shell.execute_reply.started": "2022-07-27T13:47:40.888715Z"
"iopub.execute_input": "2022-07-27T17:43:23.108610Z",
"iopub.status.busy": "2022-07-27T17:43:23.108151Z",
"iopub.status.idle": "2022-07-27T17:43:23.115550Z",
"shell.execute_reply": "2022-07-27T17:43:23.114076Z",
"shell.execute_reply.started": "2022-07-27T17:43:23.108570Z"
},
"tags": []
},
"outputs": [],
"source": [
"# for test and select\n",
"# ls_sample = [\n",
"# \"Hi-C_auxin-2days_rep1\",\n",
"# \"Hi-C_auxin-2days_rep2\",\n",
"# \"Hi-C_untreated_rep1\",\n",
"# \"Hi-C_untreated_rep2\",\n",
"# \"Hi-C_washoff-2days_rep1\",\n",
"# \"Hi-C_washoff-2days_rep2\",\n",
"# \"SRR400264_00\", # for test\n",
"# \"SRR400264_01\", # for test\n",
"# ]"
"ls_sample = [\n",
" \"Hi-C_auxin-2days_rep1\",\n",
" \"Hi-C_auxin-2days_rep2\",\n",
" \"Hi-C_untreated_rep1\",\n",
" \"Hi-C_untreated_rep2\",\n",
" \"Hi-C_washoff-2days_rep1\",\n",
" \"Hi-C_washoff-2days_rep2\",\n",
" \"SRR400264_00\", # for test\n",
" \"SRR400264_01\", # for test\n",
"]"
]
},
{
"cell_type": "code",
"execution_count": 21,
"execution_count": 32,
"id": "35072afb-e5ac-4f30-953e-d563f9af26e1",
"metadata": {
"execution": {
"iopub.execute_input": "2022-07-27T13:47:51.568431Z",
"iopub.status.busy": "2022-07-27T13:47:51.567918Z",
"iopub.status.idle": "2022-07-27T13:47:51.579808Z",
"shell.execute_reply": "2022-07-27T13:47:51.578672Z",
"shell.execute_reply.started": "2022-07-27T13:47:51.568387Z"
"iopub.execute_input": "2022-07-27T17:43:24.923365Z",
"iopub.status.busy": "2022-07-27T17:43:24.922706Z",
"iopub.status.idle": "2022-07-27T17:43:24.940585Z",
"shell.execute_reply": "2022-07-27T17:43:24.938807Z",
"shell.execute_reply.started": "2022-07-27T17:43:24.923292Z"
},
"tags": []
},
Expand Down Expand Up @@ -392,10 +402,12 @@
" 50000000,\n",
" 100000000],\n",
" 'chr_sizes': 'program/HiC-Pro_3.1.0/annotation/chrom_mm39.sizes',\n",
" 'digest_bed': 'program/HiC-Pro_3.1.0/annotation/HindIII_resfrag_mm39.bed'}"
" 'digest_bed': 'program/HiC-Pro_3.1.0/annotation/HindIII_resfrag_mm39.bed',\n",
" 'restriction_sequence': 'AAGCTT',\n",
" 'dangling_sequence': 'AGCT'}"
]
},
"execution_count": 21,
"execution_count": 32,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -414,21 +426,23 @@
" \"bin_sizes\": bin_sizes,\n",
" \"chr_sizes\": chr_sizes,\n",
" \"digest_bed\": digest_bed,\n",
" \"restriction_sequence\": restriction_sequence,\n",
" \"dangling_sequence\": dangling_sequence,\n",
"}\n",
"dt"
]
},
{
"cell_type": "code",
"execution_count": 22,
"execution_count": 33,
"id": "ad8ff845-a543-40ca-b613-867d938038b1",
"metadata": {
"execution": {
"iopub.execute_input": "2022-07-27T13:47:52.453183Z",
"iopub.status.busy": "2022-07-27T13:47:52.452656Z",
"iopub.status.idle": "2022-07-27T13:47:52.462492Z",
"shell.execute_reply": "2022-07-27T13:47:52.461347Z",
"shell.execute_reply.started": "2022-07-27T13:47:52.453137Z"
"iopub.execute_input": "2022-07-27T17:43:26.817920Z",
"iopub.status.busy": "2022-07-27T17:43:26.817217Z",
"iopub.status.idle": "2022-07-27T17:43:26.843921Z",
"shell.execute_reply": "2022-07-27T17:43:26.842137Z",
"shell.execute_reply.started": "2022-07-27T17:43:26.817857Z"
},
"tags": []
},
Expand Down
Loading

0 comments on commit a271f4d

Please sign in to comment.