https://sourceforge.net/p/phacro/wiki/Home/Recent changes to HomeenSat, 12 Oct 2013 08:39:39 -0000https://sourceforge.net/p/phacro/wiki/Home/<div class="markdown_content"><p>Brief instruction for package phacro:</p> <p>This is the first release v1.0 of package phacro. All the programs used for analyzing the oocyte single cell sequencing data are shown in this package, which are written in either perl or C++ computer language. The perl programs are packaged into a tar-ball "perl-scripts", while the C++ source code of each core program are packaged seperately. The pipeline programs as well as the invoked core programs are listed below: </p> <h1 id="1-mapping-the-sequencing-reads-to-human-reference-genome">1. mapping the sequencing reads to human reference genome</h1> <p>reads_mapping_oocyte_pipeline.pl the pipeline <br /> bwa/samtools public software, <a href="http://bio-bwa.sourceforge.net/">http://bio-bwa.sourceforge.net/</a><br /> <a href="http://samtools.sourceforge.net/">http://samtools.sourceforge.net/</a><br /> trim_malbac_adapter_lowqual core program to trim contaminated adapters and primers in the reads</p> <h1 id="2-genotype-calling-for-each-oocyte-cell-and-heterozygous-snp-calling-for-the-donor">2. genotype calling for each oocyte cell and heterozygous SNP calling for the donor</h1> <p>snp_calling_oocyte_pipeline_part1.pl the pipeline for genotype calling of each oocyte cell<br /> snp_calling_oocyte_pipeline_part2.pl the pipeline for heterozygous SNP calling of the donor<br /> gametesnp core program to calculate the genotype likelihoods</p> <h1 id="3-phasing-the-donors-haplotype-with-her-haploid-oocyte-cells">3. phasing the donor's haplotype with her haploid oocyte cells</h1> <p>hetsnp_phasing_oocyte_pipeline.pl the pipeline, phasing by dynamic programming algorithm<br /> phasing_by_pairwise_hmm.pl the pipeline, phasing by inferring pairwise crossovers and merging SNPs<br /> pairwisehmm core program, identify pairwise crossovers by hidden markov model</p> <h1 id="4-infer-crossover-positions-on-each-sequenced-oocyte-cell">4. infer crossover positions on each sequenced oocyte cell</h1> <p>crossover_inferring_oocyte_pipeline.pl the pipeline, infering crossover positions on each cell <br /> cohmm core program, infer crossover positions by hidden markov model</p> <h1 id="5-infer-chromosome-copy-number-and-identify-aneuploidy-in-oocytes">5. infer chromosome copy number and identify aneuploidy in oocytes</h1> <p>aneuploidy_normalization_factor_HMM.pl the pipeline, generate the normalization factor file<br /> infer_aneuploidy_HMM_pipeline.pl the pipeline, infer aneuploidy on the oocyte cells<br /> cnvhmm core program, infer copy number by Hidden Markov Model</p> <h1 id="6-draw-the-figures-for-oocyte-cells-include-haplotype-crossover-and-aneuploidy-information">6. draw the figures for oocyte cells include haplotype, crossover and aneuploidy information</h1> <p>haplotype_drawing_pipeline_figures.pl the pipeline, draw figures for manual curation </p> <p>The detailed instructions and usage of each programs can be found by running the program with option "--help" or "-h". More details about the algorithms can be found in the oocyte single cell sequencing paper as well as the related reference papers. If you have other questions or meet problems, please contact: Fanwei; email: fanwei@pku.edu.cn ; Address: Biodynamic Optical Imaging Center, Peking University. </p> <p>Any suggestions are welcome to improve this software phacro! Thanks very much for your attention and support!</p></div>Wei FanSat, 12 Oct 2013 08:39:39 -0000https://sourceforge.net1e4ea4349745ef6c5b29c6e855c14c5cae0ac4c8https://sourceforge.net/p/phacro/wiki/Home/<div class="markdown_content"><p>Welcome to your wiki!</p> <p>This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: <span>[SamplePage]</span>.</p> <p>The wiki uses <a class="" href="/p/phacro/wiki/markdown_syntax/">Markdown</a> syntax.</p> <p><h6>Project Members:</h6> <ul class="md-users-list"> <li><a href="/u/fanweipku/">Wei Fan</a> (admin)</li> </ul><br /> </p><p><span class="download-button-52581a35909547662b00858a" style="margin-bottom: 1em; display: block;"></span></p></div>Wei FanFri, 11 Oct 2013 15:33:09 -0000https://sourceforge.net47a3338006f57393177f78afdbcca1f14a8a4ab3