Yingzi Zhang 张樱子

icon indicating an email [email protected]

icon company King Abdullah University of Science and Technology icon location Saudi Arabia icon location Ph.D. student, bioscience@KAUST Alumna@Wuhan University, @University of Chinese Academy of Sciences, @University of Southern Denmark

Results 6 comments of Yingzi Zhang 张樱子

RGT-Hint footprinting and differential analysis output

Hi @lzj1769 , I used `rgt-hint` to do footprinting analysis. The command I used was `rgt-hint differential --organism hg38 --bc --nc 20 --standardize --mpbs-files condition1.bed,condition2.bed --reads-files condition1.bam,condition2.bam --conditions condition1,condition2 --output-prefix...

RGT-Hint footprinting and differential analysis output

> @minashaigan > > Any ideas about this issue? Dear Zhijian, Thank you very much for the reply. I am looking forward to your feedback! If it is more suggested...

RGT-Hint footprinting and differential analysis output

Hi @minashaigan and @lzj1769 , Thank you for the answering. DifferentialAnalysis.py greatly helps also. My customizing plot works very well. Many thanks, Yingzi

Can ASCIIGenome filter reads having indels on a specific genomic region?

Hi Dario, I tried ``` goto chr11:2699098-2699099 filterVariantReads -r 2699098+1 awk '$CIGAR ~ "I" || $CIGAR ~ "D"' print > test.chr11:2699098-2699099.SV.txt ``` The awk `'$CIGAR ~ "I" || $CIGAR ~...

Can ASCIIGenome filter reads having indels on a specific genomic region?

> This should keep reads having a variant at 2699098+1 AND and indel somewhere else, not necessarily at 2699098+1, though. To clarify, I need to keep reads having indels at...

all context methylation visualization

> I think the error is the same bug @wdecoster noted in #31. Hopefully a resolution can be found there. > > The bedgraph input to methplotlib is slightly different...