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Methylation profile for large genome organisms #131

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awieeeee opened this issue Mar 8, 2022 · 5 comments
Open

Methylation profile for large genome organisms #131

awieeeee opened this issue Mar 8, 2022 · 5 comments

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@awieeeee
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awieeeee commented Mar 8, 2022

Dear dpryan79,

I am trying to analyze methylation profiles of a large genome organism ( about 5Gb).
Reads were mapped using bwa-meth.
Since some of its chromosome lengths were more than 512Mb (http://www.htslib.org/doc/samtools-index.html) , bam index files were generated by samtools using a -c option.
Methyldackel extract command ran without errors but the methylation profiles were abnormally low.
Since Methyldackel properly worked with normal size organisms (such as rice), csi indexed files might cause this problem.

I would like to know to solve the problem.

Thank you very much.
@awieeeee awieeeee changed the title Methylation profile of large genome Methylation profile for large genome organisms Mar 8, 2022
@dpryan79
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dpryan79 commented Mar 8, 2022 •
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Define "abnormally low". Have you spot-checked a few regions to see if they're correct. There's no a priori reason this shouldn't work.

@awieeeee
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awieeeee commented Mar 8, 2022 •
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The boxplot indicates average methylation levels in each bin (100kb bin for rice and 1Mb for the large genome organism).
In the case of rice, both methylation callers show very similar patterns. Meanwhile, only bismark seemed to work normally.
methylation_caller.pdf

@dpryan79
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dpryan79 commented Mar 8, 2022

Hmm, OK, that does look odd. I'll look into this.

@dpryan79
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dpryan79 commented Mar 8, 2022

Can you suggest any public dataset or other data source I can use for debugging this?

@awieeeee
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Sorry for taking a time to find appropriate datasets.
For your informatin, following the current analysis environments.

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
alsa-lib                  1.2.3                h516909a_0    conda-forge
bismark                   0.23.1               hdfd78af_0    bioconda
bowtie                    1.3.0            py36hf1ae8f4_1    bioconda
bowtie2                   2.4.1            py36h5202f60_3    bioconda
bwa                       0.7.17               h5bf99c6_8    bioconda
bwameth                   0.2.3              pyh5e36f6f_0    bioconda
bz2file                   0.98                       py_0    conda-forge
bzip2                     1.0.8                h516909a_3    conda-forge
c-ares                    1.18.1               h7f8727e_0  
ca-certificates           2021.10.26           h06a4308_2  
cairo                     1.16.0            h3fc0475_1005    conda-forge
certifi                   2021.5.30        py36h06a4308_0  
curl                      7.80.0               h7f8727e_0  
cutadapt                  1.18             py36h14c3975_1    bioconda
fontconfig                2.13.1            h1056068_1002    conda-forge
freetype                  2.10.2               he06d7ca_0    conda-forge
gettext                   0.19.8.1          hc5be6a0_1002    conda-forge
giflib                    5.2.1                h516909a_2    conda-forge
glib                      2.66.1               he1b5a44_1    conda-forge
graphite2                 1.3.13            he1b5a44_1001    conda-forge
gsl                       2.5                  h294904e_1    conda-forge
harfbuzz                  2.7.2                hee91db6_0    conda-forge
hisat2                    2.2.1                h1b792b2_3    bioconda
htslib                    1.14                 h9093b5e_0    bioconda
icu                       67.1                 he1b5a44_0    conda-forge
jpeg                      9d                   h516909a_0    conda-forge
k8                        0.2.5                he513fc3_0    bioconda
krb5                      1.19.2               hac12032_0  
lcms2                     2.11                 hbd6801e_0    conda-forge
ld_impl_linux-64          2.34                 hc38a660_9    conda-forge
libblas                   3.8.0               17_openblas    conda-forge
libcblas                  3.8.0               17_openblas    conda-forge
libcurl                   7.80.0               h0b77cf5_0  
libdeflate                1.7                  h27cfd23_5  
libedit                   3.1.20210714         h7f8727e_0  
libev                     4.33                 h516909a_0    conda-forge
libffi                    3.2.1             he1b5a44_1007    conda-forge
libgcc                    7.2.0                h69d50b8_2    conda-forge
libgcc-ng                 11.2.0              h1d223b6_12    conda-forge
libgfortran-ng            7.5.0               hdf63c60_16    conda-forge
libglib                   2.66.1               h0dae87d_1    conda-forge
libgomp                   11.2.0              h1d223b6_12    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
liblapack                 3.8.0               17_openblas    conda-forge
libnghttp2                1.46.0               hce63b2e_0  
libopenblas               0.3.10          pthreads_hb3c22a3_4    conda-forge
libpng                    1.6.37               hed695b0_2    conda-forge
libssh2                   1.9.0                hab1572f_5    conda-forge
libstdcxx-ng              9.3.0               hdf63c60_16    conda-forge
libtiff                   4.1.0                hc7e4089_6    conda-forge
libuuid                   2.32.1            h14c3975_1000    conda-forge
libwebp-base              1.1.0                h516909a_3    conda-forge
libxcb                    1.13              h14c3975_1002    conda-forge
libxml2                   2.9.10               h68273f3_2    conda-forge
libzlib                   1.2.11            h36c2ea0_1013    conda-forge
lz4-c                     1.9.2                he1b5a44_3    conda-forge
methyldackel              0.6.1                h29dff0a_1    bioconda
methylpy                  1.4.3            py36h41a55b7_0    bioconda
minimap2                  2.17                 hed695b0_3    bioconda
mysql-connector-c         6.1.6                         2    bioconda
ncurses                   6.2                  he1b5a44_1    conda-forge
numpy                     1.19.1           py36h3849536_2    conda-forge
openjdk                   11.0.8               hacce0ff_0    conda-forge
openssl                   1.1.1m               h7f8727e_0  
pcre                      8.44                 he1b5a44_0    conda-forge
perl                      5.30.3               h516909a_0    conda-forge
picard                    2.18.29                       0    bioconda
pigz                      2.3.4                hed695b0_1    conda-forge
pip                       20.2.2                     py_0    conda-forge
pixman                    0.38.0            h516909a_1003    conda-forge
pthread-stubs             0.4               h14c3975_1001    conda-forge
pysam                     0.17.0           py36h61e5637_0    bioconda
python                    3.6.11          h4d41432_2_cpython    conda-forge
python_abi                3.6                     1_cp36m    conda-forge
readline                  8.0                  he28a2e2_2    conda-forge
samtools                  1.14                 hb421002_0    bioconda
scipy                     1.5.2            py36h3a855aa_0    conda-forge
setuptools                50.0.0           py36h9f0ad1d_0    conda-forge
sqlite                    3.33.0               h4cf870e_0    conda-forge
tbb                       2020.1               hc9558a2_0    conda-forge
tk                        8.6.10               hed695b0_0    conda-forge
toolshed                  0.4.6              pyh864c0ab_3    bioconda
ucsc-bigwigtowig          357                           1    bioconda
ucsc-fatotwobit           357                           1    bioconda
ucsc-twobitinfo           357                           1    bioconda
ucsc-wigtobigwig          357                           1    bioconda
wheel                     0.35.1             pyh9f0ad1d_0    conda-forge
xopen                     0.7.3                      py_0    bioconda
xorg-fixesproto           5.0               h14c3975_1002    conda-forge
xorg-inputproto           2.3.2             h14c3975_1002    conda-forge
xorg-kbproto              1.0.7             h14c3975_1002    conda-forge
xorg-libice               1.0.10               h516909a_0    conda-forge
xorg-libsm                1.2.3             h84519dc_1000    conda-forge
xorg-libx11               1.6.12               h516909a_0    conda-forge
xorg-libxau               1.0.9                h14c3975_0    conda-forge
xorg-libxdmcp             1.1.3                h516909a_0    conda-forge
xorg-libxext              1.3.4                h516909a_0    conda-forge
xorg-libxfixes            5.0.3             h516909a_1004    conda-forge
xorg-libxi                1.7.10               h516909a_0    conda-forge
xorg-libxrender           0.9.10            h516909a_1002    conda-forge
xorg-libxtst              1.2.3             h516909a_1002    conda-forge
xorg-recordproto          1.14.2            h516909a_1002    conda-forge
xorg-renderproto          0.11.1            h14c3975_1002    conda-forge
xorg-xextproto            7.3.0             h14c3975_1002    conda-forge
xorg-xproto               7.0.31            h14c3975_1007    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
zlib                      1.2.11            h36c2ea0_1013    conda-forge
zstd                      1.4.5                h6597ccf_2    conda-forge

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@dpryan79 @awieeeee