|
|
发表于 2022-9-22 19:48:28
|
显示全部楼层
Probe of FISH-quant
https://bitbucket.org/muellerflorian/fish_quant/src/master/Oligostan/Oligostan.r
If you want to use " Use of RepeatMasker Filter ", the Linux platform may be as well. MAC that so expensive that I cannot use it.
wget http://www.repeatmasker.org/RepeatMasker/RepeatMasker-4.1.2-p1.tar.gz
wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/rmblast/2.2.28/ncbi-rmblastn-2.2.28-src.tar.gz
file error by wget and solve it with curl -o xxx url.
curl -o daf ftp://ftp.ncbi.nlm.nih.gov/blast/executables/rmblast/2.2.28/ncbi-rmblastn-2.2.28-src.tar.gztar xzvf ncbi-rmblastn-2.2.28-src.tar.gztar xzvf RepeatMasker-4.1.2-p1.tar.gz
cd RepeatMaskerchmod -R 777 *./configure
Remember to download TRF software and filed with fill path
https://objects.githubusercontent.com/github-production-release-asset-2e65be/253959277/08d4c580-b9e6-11ea-96c1-2c1b402554d5?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220426%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220426T040238Z&X-Amz-Expires=300&X-Amz-Signature=f4a471086d00ffc2460e5e47575a3f0555026d8226c7795a30d05f5751bea68f&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=253959277&response-content-disposition=attachment%3B%20filename%3Dtrf409.linux64&response-content-type=application%2Foctet-stream./configure## filed with this path{your path}/trf409.linux64
select 2 to configure and then YES until end.
install R packages
install.packages ("zoo","ade4","seqinr")
- [ ] > install python module
Resolve above all and configure again
That‘s all
**
Remember to update HMMER & DFAM so that your filter more specific OR you can use blast to align with your reference genome to filter.** |
|
