liufuyan2016

How to reroot the tree?

1

Dear professor, I want to re root the tree according to the out group assigned. I use the FigTree Reroot function, the results is good. However I use R package...

Dear, I use AUGUTUS for gene prediction. I found when I want to use UTR training for prediction, the running is very lower and redundant. I check the code and...

Could I use to these AAB kmer to make evaluation the assembled phased genome?

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I have troubles understanding my smudgeplot. it look like this:  How to classified the kmer pairs into AA and AB from the results ? Could I use to theses...

三倍体基因组

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 老师，您好 三倍体基因组划分成这样了，单套17条，还能有改善吗

.hic file produced by hicpro2juicebox.sh could not used for TAD calling use juicer

1

**First, convert valid file to .hic file:** sh HiC-Pro_2.10.0/bin/utils/hicpro2juicebox.sh -i ../../test -g Project/AT/Interaction/QC/AT.fa.len -j HiC-Pro_2.10.0/bin/utils/juicer_tools.1.7.6_jcuda.0.8.jar -o ./ -b 5000 Generating Juicebox input files ... Running Juicebox ... /share/nas2/genome/biosoft/java/jdk/1.8.0_31/bin/java -jar HiC-Pro_2.10.0/bin/utils/juicer_tools.1.7.6_jcuda.0.8.jar...

Hi, I want to draw heatmap as below. The heatmap was showing two methods (one is Hi-C ,another is TAC-C) in one picture.  How to make it ? I...

Dear, How to add PCA value as in below picture? Thank you! 

hic_matrixplot plot all chromosome?

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Could hic_matrixplot plot all chromosome interaction heatmap instead of only one chromosome? Thank you!

Use custom score matrix error？

1

Dear， I use custom score matrix below :  and running the below command use diamond v2.1.9.163 : **diamond blastp --more-sensitive -d dataset.fa -q query.part_001.fa -p 5 -f 6 qseqid...