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@@ -34,17 +34,17 @@ If you want to use these data, please contact Xiaofei Yang, [email protected] o | |
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| - The files in the analysis_scripts as following: | ||
| - nextdenovo_run.pbs : the script used to assembly P. setigerum and P. rhoeas gneome based on Nanopore sequencing data by [NextDenovo](https://github.com/Nextomics/NextDenovo) | ||
| - scaffHic_breakhic_run.sh : the script used to break the contigs with missing assembly based on Hi-C data by [scaffHic](https://github.com/wtsi-hpag/scaffHiC) | ||
| - 3d-DNA-whole_pipeline.sh : the script used to scaffold genomes based on Hi-C data by [3d-DNA](https://github.com/aidenlab/3d-dna) | ||
| - purge_dups-whole-pipeline.sh : the script used to purge duplications in P. rhoease genome by [purge_dups](https://github.com/dfguan/purge_dups) | ||
| - P. rohoeas-Purge_dups-cutoffs : the `cutoffs` parameters used in P. rhoeas genome purge_dups | ||
| - busco3_evaluation.sh : [busco](https://busco-archive.ezlab.org/v3/) evaluation of the genome assembly | ||
| - repetmolder_run.sh : script used to construt own repeat library by [RepeatMolder](http://www.repeatmasker.org/RepeatModeler/) | ||
| - maker_anno.sh : Annotation genomes by [MAKER](http://www.yandell-lab.org/software/maker.html) pipeline | ||
| - maker_bopts.ctl : MAKER control file | ||
| - maker_exe.ctl : MAKER control file | ||
| - maker_opts.ctl : MAKER control file | ||
| - kaks_calculator_run.sh : Ks calculation by [Kaks_calculator](https://bigd.big.ac.cn/tools/kaks) | ||
| - mcscanx_run.sh : McscanX analysis of genome by [Mcscanx](https://github.com/wyp1125/MCScanx) | ||
| - trinity_run.pbs : script used to assembly transcripts based on RNA-seq data by [trinity](https://rnabio.org/module-06-trinity/0006/02/01/Trinity_Assembly_And_Analysis/) | ||
| - RNA-seq_analysis.sh : script used to calculate `TPM` based on RNA-seq data by [hisat2](https://daehwankimlab.github.io/hisat2/), [stringtie](http://ccb.jhu.edu/software/stringtie/) and [ballgown](https://github.com/alyssafrazee/ballgown) | ||
| - `scaffHic_breakhic_run.sh` : the script used to break the contigs with missing assembly based on Hi-C data by [scaffHic](https://github.com/wtsi-hpag/scaffHiC) | ||
| - `3d-DNA-whole_pipeline.sh` : the script used to scaffold genomes based on Hi-C data by [3d-DNA](https://github.com/aidenlab/3d-dna) | ||
| - `purge_dups-whole-pipeline.sh` : the script used to purge duplications in P. rhoease genome by [purge_dups](https://github.com/dfguan/purge_dups) | ||
| - `P. rohoeas-Purge_dups-cutoffs` : the `cutoffs` parameters used in P. rhoeas genome purge_dups | ||
| - `busco3_evaluation.sh` : [busco](https://busco-archive.ezlab.org/v3/) evaluation of the genome assembly | ||
| - `repetmolder_run.sh` : script used to construt own repeat library by [RepeatMolder](http://www.repeatmasker.org/RepeatModeler/) | ||
| - `maker_anno.sh` : Annotation genomes by [MAKER](http://www.yandell-lab.org/software/maker.html) pipeline | ||
| - `maker_bopts.ctl` : MAKER control file | ||
| - `maker_exe.ctl` : MAKER control file | ||
| - `maker_opts.ctl` : MAKER control file | ||
| - `kaks_calculator_run.sh` : Ks calculation by [Kaks_calculator](https://bigd.big.ac.cn/tools/kaks) | ||
| - `mcscanx_run.sh` : McscanX analysis of genome by [Mcscanx](https://github.com/wyp1125/MCScanx) | ||
| - `trinity_run.pbs` : script used to assembly transcripts based on RNA-seq data by [trinity](https://rnabio.org/module-06-trinity/0006/02/01/Trinity_Assembly_And_Analysis/) | ||
| - `RNA-seq_analysis.sh` : script used to calculate `TPM` based on RNA-seq data by [hisat2](https://daehwankimlab.github.io/hisat2/), [stringtie](http://ccb.jhu.edu/software/stringtie/) and [ballgown](https://github.com/alyssafrazee/ballgown) | ||