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Third party softwares
Zhiao Shi edited this page Jul 20, 2021
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To run this total RNAseq analysis pipeline, your server should have Perl and R installed. The pipeline also needs Samtools, BWA, CIRI Bowtie2 and ESRM installed and in your Path.
- Samtools V1.10 or later is required.
- Samtools should be installed and in your Path.
- Samtools can be found on Github: https://github.com/samtools/samtools.
- BWA V0.7.17 is required for this pipeline.
- It can be downloaded from https://github.com/lh3/bwa/releases/tag/v0.7.17 .
- CIRI V2.0.6 is needed for circRNA calling.
- It can be downloaded from sourceforge https://sourceforge.net/projects/ciri/files/CIRI2/
- Bowtie2 V2.3.3 is required for this pipeline.
- It can be downloaded from https://github.com/BenLangmead/bowtie2/releases/tag/v2.3.3
- RSEM V1.3.1 is required
- It can be downloaded from https://github.com/deweylab/RSEM/releases/tag/v1.3.1