diff --git a/code/07_Fig2_tad_borders_properties_part1.ipynb b/code/07_Fig2_tad_borders_properties_part1.ipynb
index 8de2e90..e6e804f 100644
--- a/code/07_Fig2_tad_borders_properties_part1.ipynb
+++ b/code/07_Fig2_tad_borders_properties_part1.ipynb
@@ -49,8 +49,8 @@
     "boundaries_plus[\"border_num1\"]= range(1,boundaries_plus.shape[0] + 1)\n",
     "boundaries_minus[\"border_num2\"]= range(1,boundaries_minus.shape[0] + 1)\n",
     "\n",
-    "boundaries_minus_sploped = pbt.from_dataframe(boundaries_minus).slop(b=22_500, g=\"../data/chrom.sizes\")\n",
-    "boundaries_plus_sploped = pbt.from_dataframe(boundaries_plus).slop(b=22_500, g=\"../data/chrom.sizes\")"
+    "boundaries_minus_sploped = pbt.from_dataframe(boundaries_minus).slop(b=22_500, g=\"../data/hg38.chrom.sizes\")\n",
+    "boundaries_plus_sploped = pbt.from_dataframe(boundaries_plus).slop(b=22_500, g=\"../data/hg38.chrom.sizes\")"
    ]
   },
   {
diff --git a/code/08_Fig2_tad_and_thier_borders_properties_part2.ipynb b/code/08_Fig2_tad_and_thier_borders_properties_part2.ipynb
index 2168d42..459328d 100644
--- a/code/08_Fig2_tad_and_thier_borders_properties_part2.ipynb
+++ b/code/08_Fig2_tad_and_thier_borders_properties_part2.ipynb
@@ -762,8 +762,8 @@
     }
    ],
    "source": [
-    "boundaries_minus_sploped = pbt.from_dataframe(boundaries_minus.iloc[:, [0,1,2, 5]]).slop(b=15000, g=\"../data/chrom.sizes\")\n",
-    "boundaries_plus_sploped = pbt.from_dataframe(boundaries_plus.iloc[:, [0,1,2, 5]]).slop(b=15000,g=\"../data/chrom.sizes\")"
+    "boundaries_minus_sploped = pbt.from_dataframe(boundaries_minus.iloc[:, [0,1,2, 5]]).slop(b=15000, g=\"../data/hg38.chrom.sizes\")\n",
+    "boundaries_plus_sploped = pbt.from_dataframe(boundaries_plus.iloc[:, [0,1,2, 5]]).slop(b=15000,g=\"../data/hg38.chrom.sizes\")"
    ]
   },
   {
@@ -774,7 +774,7 @@
    "outputs": [],
    "source": [
     "def make_tss(pc_DE_genes_minus):\n",
-    "    chrom_sizes_path = \"../data/chrom.sizes\"\n",
+    "    chrom_sizes_path = \"../data/hg38.chrom.sizes\"\n",
     "    tss = pbt.from_dataframe(pc_DE_genes_minus).flank(g=chrom_sizes_path, s=True, l=1, r=0)\n",
     "    tss = pd.read_table(tss.fn, header = None, names=pc_DE_genes_minus.columns.tolist())\n",
     "    return tss\n",
@@ -904,7 +904,7 @@
    "outputs": [],
    "source": [
     "def make_a_b(expressed_not_de, border_file_init):  \n",
-    "    border_file_slopped = pbt.from_dataframe(border_file_init.iloc[:, [0,1,2, 5]]).slop(b=15000, g=\"../data/chrom.sizes\")\n",
+    "    border_file_slopped = pbt.from_dataframe(border_file_init.iloc[:, [0,1,2, 5]]).slop(b=15000, g=\"../data/hg38.chrom.sizes\")\n",
     "\n",
     "    b_noDE = border_file_slopped\\\n",
     "                  .intersect(pbt.from_dataframe(expressed_not_de), wa=True, wb=True)\n",
diff --git a/code/09_Fig3_chromtain_loops_properties.ipynb b/code/09_Fig3_chromtain_loops_properties.ipynb
index 4651292..91632f1 100644
--- a/code/09_Fig3_chromtain_loops_properties.ipynb
+++ b/code/09_Fig3_chromtain_loops_properties.ipynb
@@ -726,7 +726,7 @@
    "source": [
     "columns = [\"chrom\",\"start\",\"end\",\"gene.name\", \"gene.id\",\"strand\"]\n",
     "columns2 = ['chrom', 'start', 'end', 'gene.name', 'log2FC', 'strand']\n",
-    "chrom_sizes_path = '../data/chrom.sizes' #set path to chrom.sizes\n",
+    "chrom_sizes_path = '../data/hg38.chrom.sizes' \n",
     "tss_plus = pbt.from_dataframe(de_neurons).flank(g=chrom_sizes_path, s=True, l=2000, r=0)\n",
     "tss_plus = pd.read_table(tss_plus.fn, header = None, names=columns2)\n",
     "\n",
@@ -756,7 +756,7 @@
     "    df = pd.concat([df_sel[[\"chrom1\",\"start1\", \"end1\"]],\n",
     "          df_sel[[\"chrom2\",\"start2\", \"end2\"]].rename(columns = {\"chrom2\":\"chrom1\",\"start2\":\"start1\",\"end2\":\"end1\"})])\n",
     "    df = df.drop_duplicates().reset_index(drop=True)  \n",
-    "    df =pbt.from_dataframe(df).slop(b=slop, g=\"../data/chrom.sizes\")\n",
+    "    df =pbt.from_dataframe(df).slop(b=slop, g=\"../data/hg38.chrom.sizes\")\n",
     "    \n",
     "    colnames = de_neurons.columns.tolist()    \n",
     "    df_intersect = pbt.from_dataframe(de_neurons)\\\n",
@@ -890,7 +890,7 @@
     "    df_processed = df[columns].reset_index(drop=True)\n",
     "    df_processed[\"anchor\"] = anchor    \n",
     "    if slopvalue and slopvalue > 0:\n",
-    "        df_slopped = pbt.from_dataframe(df_processed).slop(b=slopvalue, g='../data/chrom.sizes')\n",
+    "        df_slopped = pbt.from_dataframe(df_processed).slop(b=slopvalue, g='../data/hg38.chrom.sizes')\n",
     "        df_processed = pd.read_table(df_slopped.fn, header=None, names=df_processed.columns.tolist())\n",
     "        assert df_processed.shape[0] > 1, \"Dataframe after slopping has less than 2 rows.\"\n",
     "    \n",
diff --git a/data/chrom.sizes b/data/chrom.sizes
deleted file mode 100644
index bbd5557..0000000
--- a/data/chrom.sizes
+++ /dev/null
@@ -1,25 +0,0 @@
-chr1	248956422
-chr2	242193529
-chr3	198295559
-chr4	190214555
-chr5	181538259
-chr6	170805979
-chr7	159345973
-chr8	145138636
-chr9	138394717
-chr10	133797422
-chr11	135086622
-chr12	133275309
-chr13	114364328
-chr14	107043718
-chr15	101991189
-chr16	90338345
-chr17	83257441
-chr18	80373285
-chr19	58617616
-chr20	64444167
-chr21	46709983
-chr22	50818468
-chrX	156040895
-chrY	57227415
-chrM	16569
diff --git a/env2.yml b/env2.yml
index 4a6aa7d..6fa00d2 100644
--- a/env2.yml
+++ b/env2.yml
@@ -6,166 +6,161 @@ channels:
   - conda-forge
   - https://mirrors.ustc.edu.cn/anaconda/pkgs/main/
 dependencies:
-  - _libgcc_mutex=0.1=conda_forge
-  - _openmp_mutex=4.5=2_kmp_llvm
-  - asciitree=0.3.3=py_2
-  - bedtools=2.30.0=h468198e_3
-  - biopython=1.79=py39hb9d737c_3
-  - blas=1.0=openblas
-  - blosc=1.21.0=h4ff587b_1
-  - bokeh=2.4.3=pyhd8ed1ab_3
-  - bowtie2=2.2.5=py39h7cff6ad_8
-  - brotlipy=0.7.0=py39h27cfd23_1003
-  - bwa-mem2=2.2.1=hd03093a_3
-  - bzip2=1.0.8=h7f98852_4
-  - c-ares=1.18.1=h7f98852_0
-  - ca-certificates=2023.12.12=h06a4308_0
-  - cached-property=1.5.2=hd8ed1ab_1
-  - cached_property=1.5.2=pyha770c72_1
-  - certifi=2023.11.17=py39h06a4308_0
-  - cffi=1.15.0=py39hd667e15_1
-  - charset-normalizer=2.0.4=pyhd3eb1b0_0
-  - click=8.1.3=unix_pyhd8ed1ab_2
-  - cloudpickle=2.2.0=pyhd8ed1ab_0
-  - colorama=0.4.4=pyhd3eb1b0_0
-  - coloredlogs=15.0.1=pyhd8ed1ab_3
-  - colormath=3.0.0=py_2
-  - commonmark=0.9.1=py_0
-  - conda=22.9.0=py39h06a4308_0
-  - conda-content-trust=0.1.1=pyhd3eb1b0_0
-  - conda-package-handling=1.8.1=py39h7f8727e_0
-  - cooler=0.8.11=pyh5e36f6f_1
-  - cryptography=36.0.0=py39h9ce1e76_0
-  - curl=7.86.0=h7bff187_0
-  - cycler=0.11.0=pyhd8ed1ab_0
-  - dask=2022.2.1=pyhd3eb1b0_0
-  - dask-core=2022.2.1=pyhd3eb1b0_0
-  - dataclasses=0.8=pyhc8e2a94_3
-  - deeptools=3.5.1=py_0
-  - deeptoolsintervals=0.1.9=py39hbf8eff0_4
-  - dill=0.3.6=pyhd8ed1ab_1
-  - distributed=2022.2.1=pyhd3eb1b0_0
-  - expat=2.5.0=h27087fc_0
-  - fastqc=0.11.9=hdfd78af_1
-  - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
-  - fontconfig=2.14.1=hc2a2eb6_0
-  - freetype=2.12.1=hca18f0e_0
-  - fsspec=2022.10.0=pyhd8ed1ab_0
-  - future=0.18.2=pyhd8ed1ab_6
-  - h5py=3.7.0=nompi_py39h63b1161_100
-  - hdf5=1.12.1=nompi_h2386368_104
-  - heapdict=1.0.1=py_0
-  - hisat2=2.2.1=h87f3376_4
-  - htslib=1.15.1=h9753748_0
-  - humanfriendly=10.0=py39hf3d152e_2
-  - icu=70.1=h27087fc_0
-  - idna=3.3=pyhd3eb1b0_0
-  - importlib-metadata=5.0.0=pyha770c72_1
-  - jinja2=3.1.2=pyhd8ed1ab_1
-  - jpeg=9e=h166bdaf_2
-  - keyutils=1.6.1=h166bdaf_0
-  - kiwisolver=1.4.4=py39hf939315_1
-  - krb5=1.19.3=h3790be6_0
-  - lcms2=2.12=hddcbb42_0
-  - ld_impl_linux-64=2.35.1=h7274673_9
-  - lerc=3.0=h9c3ff4c_0
-  - libblas=3.9.0=16_linux64_openblas
-  - libcblas=3.9.0=16_linux64_openblas
-  - libcurl=7.86.0=h7bff187_0
-  - libdeflate=1.10=h7f98852_0
-  - libedit=3.1.20191231=he28a2e2_2
-  - libev=4.33=h516909a_1
-  - libffi=3.3=he6710b0_2
-  - libgcc=7.2.0=h69d50b8_2
-  - libgcc-ng=12.2.0=h65d4601_19
-  - libgfortran-ng=12.2.0=h69a702a_19
-  - libgfortran5=12.2.0=h337968e_19
-  - libiconv=1.16=h516909a_0
-  - liblapack=3.9.0=16_linux64_openblas
-  - libnghttp2=1.47.0=hdcd2b5c_1
-  - libnsl=2.0.0=h7f98852_0
-  - libopenblas=0.3.21=pthreads_h78a6416_3
-  - libpng=1.6.38=h753d276_0
-  - libssh2=1.10.0=haa6b8db_3
-  - libstdcxx-ng=12.2.0=h46fd767_19
-  - libtiff=4.3.0=h0fcbabc_4
-  - libuuid=2.32.1=h7f98852_1000
-  - libwebp-base=1.2.4=h166bdaf_0
-  - libxml2=2.9.14=h22db469_4
-  - libzlib=1.2.13=h166bdaf_4
-  - llvm-openmp=14.0.4=he0ac6c6_0
-  - locket=1.0.0=pyhd8ed1ab_0
-  - lz4-c=1.9.3=h295c915_1
-  - lzo=2.10=h7b6447c_2
-  - lzstring=1.0.4=py_1001
-  - markdown=3.4.1=pyhd8ed1ab_0
-  - markupsafe=2.1.1=py39hb9d737c_2
-  - matplotlib-base=3.4.3=py39h2fa2bec_2
-  - mock=4.0.3=pyhd3eb1b0_0
-  - msgpack-python=1.0.4=py39hf939315_1
-  - multiprocess=0.70.14=py39hb9d737c_3
-  - ncbi-ngs-sdk=2.11.2=pl5321h629fbf0_1
-  - ncurses=6.3=h7f8727e_2
-  - networkx=2.8.7=pyhd8ed1ab_0
-  - numexpr=2.8.3=py39hd2a5715_0
-  - numpy=1.23.4=py39h3d75532_1
-  - olefile=0.46=pyh9f0ad1d_1
-  - openjdk=8.0.332=h166bdaf_0
-  - openjpeg=2.5.0=h7d73246_0
-  - openssl=1.1.1w=h7f8727e_0
-  - ossuuid=1.6.2=hf484d3e_1000
-  - packaging=21.3=pyhd8ed1ab_0
-  - pairix=0.3.7=py39h87d955d_4
-  - pandas=1.5.1=py39h4661b88_1
-  - partd=1.3.0=pyhd8ed1ab_0
-  - pip=21.2.4=py39h06a4308_0
-  - plotly=5.11.0=pyhd8ed1ab_0
-  - psutil=5.9.3=py39hb9d737c_1
-  - py2bit=0.3.0=py39hbf8eff0_6
-  - pybigwig=0.3.18=py39h792ddb7_2
-  - pycosat=0.6.3=py39h27cfd23_0
-  - pycparser=2.21=pyhd3eb1b0_0
-  - pyfaidx=0.7.1=pyh5e36f6f_0
-  - pygments=2.13.0=pyhd8ed1ab_0
-  - pyopenssl=22.0.0=pyhd3eb1b0_0
-  - pyparsing=3.0.9=pyhd8ed1ab_0
-  - pysam=0.19.1=py39h5030a8b_0
-  - pysocks=1.7.1=py39h06a4308_0
-  - pytables=3.7.0=py39h9da3b7f_0
-  - python=3.9.12=h12debd9_0
-  - python-dateutil=2.8.2=pyhd8ed1ab_0
-  - python_abi=3.9=2_cp39
-  - pytz=2022.5=pyhd8ed1ab_0
-  - pyvcf3=1.0.3=pyhdfd78af_0
-  - pyyaml=6.0=py39hb9d737c_5
-  - readline=8.1.2=h7f8727e_1
-  - requests=2.27.1=pyhd3eb1b0_0
-  - rich=12.6.0=pyhd8ed1ab_0
-  - rich-click=1.5.2=pyhd8ed1ab_0
-  - ruamel_yaml=0.15.100=py39h27cfd23_0
-  - scipy=1.9.3=py39hddc5342_1
-  - setuptools=61.2.0=py39h06a4308_0
-  - simplejson=3.17.6=py39hb9d737c_2
-  - six=1.16.0=pyhd3eb1b0_1
-  - sortedcontainers=2.4.0=pyhd8ed1ab_0
-  - spectra=0.0.11=py_1
-  - sqlite=3.38.2=hc218d9a_0
-  - tblib=1.7.0=pyhd8ed1ab_0
-  - tenacity=8.1.0=pyhd8ed1ab_0
-  - tk=8.6.11=h1ccaba5_0
-  - toolz=0.12.0=pyhd8ed1ab_0
-  - tornado=6.2=py39hb9d737c_1
-  - tqdm=4.63.0=pyhd3eb1b0_0
-  - typing_extensions=4.4.0=pyha770c72_0
-  - tzdata=2022a=hda174b7_0
-  - urllib3=1.26.8=pyhd3eb1b0_0
-  - wheel=0.37.1=pyhd3eb1b0_0
-  - xz=5.2.5=h7b6447c_0
-  - yaml=0.2.5=h7b6447c_0
-  - zict=2.2.0=pyhd8ed1ab_0
-  - zipp=3.10.0=pyhd8ed1ab_0
-  - zlib=1.2.13=h166bdaf_4
-  - zstd=1.5.2=h6239696_4
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - asciitree=0.3.3
+  - bedtools=2.30.0
+  - biopython=1.79
+  - blas=1.0
+  - blosc=1.21.0
+  - brotlipy=0.7.0
+  - bzip2=1.0.8
+  - c-ares=1.18.1
+  - ca-certificates=2023.12.12
+  - cached-property=1.5.2
+  - cached_property=1.5.2
+  - certifi=2023.11.17
+  - cffi=1.15.0
+  - charset-normalizer=2.0.4
+  - click=8.1.3
+  - cloudpickle=2.2.0
+  - colorama=0.4.4
+  - coloredlogs=15.0.1
+  - colormath=3.0.0
+  - commonmark=0.9.1
+  - conda=22.9.0
+  - conda-content-trust=0.1.1
+  - conda-package-handling=1.8.1
+  - cooler=0.8.11
+  - cryptography=36.0.0
+  - curl=7.86.0
+  - cycler=0.11.0
+  - dask=2022.2.1
+  - dask-core=2022.2.1
+  - dataclasses=0.8
+  - deeptools=3.5.1
+  - deeptoolsintervals=0.1.9
+  - dill=0.3.6
+  - distributed=2022.2.1
+  - expat=2.5.0
+  - fastqc=0.11.9
+  - font-ttf-dejavu-sans-mono=2.37
+  - fontconfig=2.14.1
+  - freetype=2.12.1
+  - fsspec=2022.10.0
+  - future=0.18.2
+  - heapdict=1.0.1
+  - hisat2=2.2.1
+  - htslib=1.15.1
+  - humanfriendly=10.0
+  - icu=70.1
+  - idna=3.3
+  - importlib-metadata=5.0.0
+  - jinja2=3.1.2
+  - jpeg=9e
+  - keyutils=1.6.1
+  - kiwisolver=1.4.4
+  - krb5=1.19.3
+  - lcms2=2.12
+  - ld_impl_linux-64=2.35.1
+  - lerc=3.0
+  - libblas=3.9.0
+  - libcblas=3.9.0
+  - libcurl=7.86.0
+  - libdeflate=1.10
+  - libedit=3.1.20191231
+  - libev=4.33
+  - libffi=3.3
+  - libgcc=7.2.0
+  - libgcc-ng=12.2.0
+  - libgfortran-ng=12.2.0
+  - libgfortran5=12.2.0
+  - libiconv=1.16
+  - liblapack=3.9.0
+  - libnghttp2=1.47.0
+  - libnsl=2.0.0
+  - libopenblas=0.3.21
+  - libpng=1.6.38
+  - libssh2=1.10.0
+  - libstdcxx-ng=12.2.0
+  - libtiff=4.3.0
+  - libuuid=2.32.1
+  - libwebp-base=1.2.4
+  - libxml2=2.9.14
+  - libzlib=1.2.13
+  - llvm-openmp=14.0.4
+  - locket=1.0.0
+  - lz4-c=1.9.3
+  - lzo=2.10
+  - lzstring=1.0.4
+  - markdown=3.4.1
+  - markupsafe=2.1.1
+  - matplotlib-base=3.4.3
+  - mock=4.0.3
+  - msgpack-python=1.0.4
+  - multiprocess=0.70.14
+  - ncurses=6.3
+  - networkx=2.8.7
+  - numexpr=2.8.3
+  - numpy=1.23.4
+  - olefile=0.46
+  - openjdk=8.0.332
+  - openjpeg=2.5.0
+  - openssl=1.1.1w
+  - ossuuid=1.6.2
+  - packaging=21.3
+  - pairix=0.3.7
+  - pandas=1.5.1
+  - partd=1.3.0
+  - pillow=8.4.0
+  - pip=21.2.4
+  - plotly=5.11.0
+  - psutil=5.9.3
+  - py2bit=0.3.0
+  - pybigwig=0.3.18
+  - pycosat=0.6.3
+  - pycparser=2.21
+  - pyfaidx=0.7.1
+  - pygments=2.13.0
+  - pyopenssl=22.0.0
+  - pyparsing=3.0.9
+  - pysam=0.19.1
+  - pysocks=1.7.1
+  - pytables=3.7.0
+  - python=3.9.12
+  - python-dateutil=2.8.2
+  - python_abi=3.9
+  - pytz=2022.5
+  - pyvcf3=1.0.3
+  - pyyaml=6.0
+  - readline=8.1.2
+  - requests=2.27.1
+  - rich=12.6.0
+  - rich-click=1.5.2
+  - ruamel_yaml=0.15.100
+  - scipy=1.9.3
+  - setuptools=61.2.0
+  - simplejson=3.17.6
+  - six=1.16.0
+  - sortedcontainers=2.4.0
+  - spectra=0.0.11
+  - sqlite=3.38.2
+  - tblib=1.7.0
+  - tenacity=8.1.0
+  - tk=8.6.11
+  - toolz=0.12.0
+  - tornado=6.2
+  - tqdm=4.63.0
+  - typing_extensions=4.4.0
+  - tzdata=2022a
+  - urllib3=1.26.8
+  - wheel=0.37.1
+  - xz=5.2.5
+  - yaml=0.2.5
+  - zict=2.2.0
+  - zipp=3.10.0
+  - zlib=1.2.13
+  - zstd=1.5.2
   - pip:
     - bioframe==0.3.3
     - coolpuppy==1.0.0