search

PacificBiosciences / pbbioconda

PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
BSD 3-Clause Clear License
243 stars 44 forks source link

Mapping MT and RP genes from 10x single cell kinnex #673

Closed ollieeknight closed 1 month ago

ollieeknight commented 3 months ago

Operating system

 cat /etc/os-release
NAME="Rocky Linux"
VERSION="8.7 (Green Obsidian)"
ID="rocky"
ID_LIKE="rhel centos fedora"
VERSION_ID="8.7"
PLATFORM_ID="platform:el8"
PRETTY_NAME="Rocky Linux 8.7 (Green Obsidian)"
ANSI_COLOR="0;32"
LOGO="fedora-logo-icon"
CPE_NAME="cpe:/o:rocky:rocky:8:GA"
HOME_URL="https://rockylinux.org/"
BUG_REPORT_URL="https://bugs.rockylinux.org/"
ROCKY_SUPPORT_PRODUCT="Rocky-Linux-8"
ROCKY_SUPPORT_PRODUCT_VERSION="8.7"
REDHAT_SUPPORT_PRODUCT="Rocky Linux"
REDHAT_SUPPORT_PRODUCT_VERSION="8.7"

Package name

pigeon 1.2.0 (commit -v1.2.0)

Using:
  pbbam     : 2.5.0 (commit v2.5.0)
  pbcopper  : 2.4.0 (commit v2.4.0)
  boost     : 1.81
  htslib    : 1.17
  zlib      : 1.2.13

Conda environment

conda list
# packages in environment at /data/gpfs-1/users/knighto_c/work/bin/miniconda3/envs/pacbio:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
avro-python3              1.10.2             pyhd8ed1ab_0    conda-forge
biopython                 1.79             py37h540881e_2    conda-forge
brotli-python             1.0.9            py37hd23a5d3_7    conda-forge
bzip2                     1.0.8                hd590300_5    conda-forge
c-ares                    1.28.1               hd590300_0    conda-forge
ca-certificates           2024.2.2             hbcca054_0    conda-forge
certifi                   2024.2.2           pyhd8ed1ab_0    conda-forge
charset-normalizer        3.3.2              pyhd8ed1ab_0    conda-forge
curl                      7.87.0               h6312ad2_0    conda-forge
htslib                    1.17                 h6bc39ce_1    bioconda
idna                      3.6                pyhd8ed1ab_0    conda-forge
iso8601                   2.1.0              pyhd8ed1ab_0    conda-forge
isoseq                    4.0.0                h9ee0642_0    bioconda
keyutils                  1.6.1                h166bdaf_0    conda-forge
krb5                      1.20.1               hf9c8cef_0    conda-forge
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
libblas                   3.9.0           21_linux64_openblas    conda-forge
libcblas                  3.9.0           21_linux64_openblas    conda-forge
libcurl                   7.87.0               h6312ad2_0    conda-forge
libdeflate                1.13                 h166bdaf_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 hd590300_2    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 13.2.0               h807b86a_5    conda-forge
libgfortran-ng            13.2.0               h69a702a_5    conda-forge
libgfortran5              13.2.0               ha4646dd_5    conda-forge
libgomp                   13.2.0               h807b86a_5    conda-forge
liblapack                 3.9.0           21_linux64_openblas    conda-forge
libnghttp2                1.51.0               hdcd2b5c_0    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libopenblas               0.3.26          pthreads_h413a1c8_0    conda-forge
libsqlite                 3.45.2               h2797004_0    conda-forge
libssh2                   1.10.0               haa6b8db_3    conda-forge
libstdcxx-ng              13.2.0               h7e041cc_5    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
lima                      2.9.0                h9ee0642_1    bioconda
ncurses                   6.4.20240210         h59595ed_0    conda-forge
numpy                     1.21.6           py37h976b520_0    conda-forge
openssl                   1.1.1w               hd590300_0    conda-forge
pbcommand                 2.1.1                      py_2    bioconda
pbcore                    2.1.2                      py_2    bioconda
pbcoretools               0.8.1                      py_1    bioconda
pbmm2                     1.13.1               h9ee0642_0    bioconda
pbpigeon                  1.2.0                h4ac6f70_0    bioconda
pbskera                   1.2.0                hdfd78af_0    bioconda
pip                       24.0               pyhd8ed1ab_0    conda-forge
pysam                     0.21.0           py37hee149a5_0    bioconda
pysocks                   1.7.1            py37h89c1867_5    conda-forge
python                    3.7.12          hb7a2778_100_cpython    conda-forge
python_abi                3.7                     4_cp37m    conda-forge
pytz                      2024.1             pyhd8ed1ab_0    conda-forge
readline                  8.2                  h8228510_1    conda-forge
requests                  2.31.0             pyhd8ed1ab_0    conda-forge
samtools                  1.18                 hd87286a_0    bioconda
setuptools                69.0.3             pyhd8ed1ab_0    conda-forge
sqlite                    3.45.2               h2c6b66d_0    conda-forge
tk                        8.6.13          noxft_h4845f30_101    conda-forge
urllib3                   2.2.1              pyhd8ed1ab_0    conda-forge
wheel                     0.42.0             pyhd8ed1ab_0    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
zlib                      1.2.13               hd590300_5    conda-forge
zstd                      1.5.5                hfc55251_0    conda-forge

Describe the bug I am trying to map mitochondrial and ribosomal genes, but they never appear in the outs/genes_seurat features.tsv file. They are in the gencode.v45..annotation.gtf I am running pigeon prepare etc with. I am running everything through from the raw files under this.

Error message None

To Reproduce I am using then gencode GTF version 45 from here

Expected behavior In normal 10x sequencing runs there is good capture of ribosomal and mitochondrial genes (around 10% and 10% respectively)

ollieeknight commented 3 months ago

Ideally I'd like to map it to an ensemble gtf that we have several other sequencing runs mapped to

armintoepfer commented 1 month ago

We can only help you with mechanical problems of our software and not result interpretation.