Last updated: 2022-02-28
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Knit directory: chipseq-cross-species/
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| html | fc28053 | lecook | 2022-02-28 | Build site. |
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For full snakemake script see code/dunnart_peak_calling/dunnart_snakefile.
# create conda environment with all packages and dependencies
conda create --name chip bowtie2 samtools picard deeptools multiqc phantompeakqualtools preseq macs2 bedtools fastqc pybedtools
# save environment to a yaml file
conda env export > chip_environment.yml
# activate environment before running pipeline
conda activate chipCluster configuration file: code/configs/cluster.json Sample configuration file: code/configs/config.yaml Sample text file: code/configs/SSR.text
module load snakemake/6.6.1
snakemake --snakemakefile code/dunnart_peak_calling/dunnart_snakefile -j 6 --cluster-config envs/cluster.json --cluster "sbatch -A {cluster.account} -t {cluster.time} -p {cluster.partition} --nodes {cluster.nodes} --ntasks {cluster.ntasks} --mem {cluster.mem}" &We can approximate effective genome size for various read lengths using the khmer program and unique-kmers.py. This will estimate the number of unique kmers (for a specified length kmer) which can be used to infer the total uniquely mappable genome. (I.e it doesn’t include highly repetitive regions). https://khmer.readthedocs.io/en/v2.1.1/user/scripts.html This was a suggestion of deepTools: https://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html
module load pip/21.2.4-python-3.8.6
pip2.7 install khmerRun unique-kmers.py on dunnart genome for read length of 150bp:
/usr/local/bin/unique-kmers.py -k 150 Scras_dunnart_assem1.0_pb-ont-illsr_flyeassem_red-rd-scfitr2_pil2xwgs2_60chr.faEstimated number of unique 150-mers in /Users/lauracook/../../Volumes/macOS/genomes/Scras_dunnart_assem1.0_pb-ont-illsr_flyeassem_red-rd-scfitr2_pil2xwgs2_60chr.fasta: 2740338543
Total estimated number of unique 150-mers: 2740338543Load modules:
module load gcc/8.3.0
module load bowtie2/2.3.5.1Build index:
bowtie2-build Scras_dunnart_assem1.0_pb-ont-illsr_flyeassem_red-rd-scfitr2_pil2xwgs2_60chr.fa Scras_dunnart_assem1.0_pb-ont-illsr_flyeassem_red-rd-scfitr2_pil2xwgs2_60chrSee full snakemake script for details: code/dunnart_peak_calling/dunnart_snakefile.
| read counts | |||||||
|---|---|---|---|---|---|---|---|
| Sample | Antibody | bowtie2 alignment | filtered reads^ | remove duplicates | NRF* | PBC1* | PBC2* |
| A-1 | input | 130587134 | 87165286 | 47645260 | 0.773602 | 0.774519 | 4.45728 |
| A-2 | H3K4me3 | 103324742 | 62678360 | 35617708 | 0.789709 | 0.789661 | 4.754989 |
| A-3 | H3K27ac | 131071676 | 86503078 | 45700530 | 0.761768 | 0.761687 | 4.196586 |
| B-1 | input | 111574640 | 72303316 | 44433864 | 0.820313 | 0.819974 | 5.545324 |
| B-2 | H3K4me3 | 114146802 | 67048994 | 42357180 | 0.831032 | 0.830749 | 5.898224 |
| B-3 | H3K27ac | 104714846 | 66615704 | 43939460 | 0.847255 | 0.847022 | 6.529168 |
| * calculated from a subsample of ~10-15M aligned reads prior to removing duplicates | |||||||
| ̂ excluded low quality (MAPQ 30) and orphaned reads |
sessionInfo()R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux
Matrix products: default
BLAS/LAPACK: /usr/local/easybuild-2019/easybuild/software/compiler/gcc/10.2.0/openblas/0.3.12/lib/libopenblas_haswellp-r0.3.12.so
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] workflowr_1.7.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 jquerylib_0.1.4 pillar_1.6.1 compiler_4.1.0
[5] bslib_0.2.5.1 later_1.2.0 git2r_0.28.0 tools_4.1.0
[9] getPass_0.2-2 digest_0.6.27 jsonlite_1.7.2 evaluate_0.14
[13] lifecycle_1.0.1 tibble_3.1.2 pkgconfig_2.0.3 rlang_1.0.1
[17] cli_2.5.0 rstudioapi_0.13 yaml_2.2.1 xfun_0.23
[21] httr_1.4.2 stringr_1.4.0 knitr_1.33 sass_0.4.0
[25] fs_1.5.0 vctrs_0.3.8 rprojroot_2.0.2 glue_1.4.2
[29] R6_2.5.0 processx_3.5.2 fansi_0.5.0 rmarkdown_2.8
[33] callr_3.7.0 magrittr_2.0.1 whisker_0.4 ps_1.6.0
[37] promises_1.2.0.1 ellipsis_0.3.2 htmltools_0.5.1.1 httpuv_1.6.1
[41] utf8_1.2.1 stringi_1.6.2 crayon_1.4.1