User: chiefcat

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chiefcat70
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Posts by chiefcat

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[ChIPSeeker] Getting overlapping genomic feature annotation (e.g. peak locate in gene A & defined TSS region of gene B)
... Hi guys, I'm trying to use ChIPseeker but couldn't find a way to call the overlapping features during peak annotation. Example: TSS setting: -3kb +500bp --> I would like to get the ChIP peak annotated with "Rrs1, 3'UTR" & "Adhfe1, TSS" I've tried a lot of different arguments but all of t ...
annotation chipseeker chip-seq written 28 days ago by chiefcat70 • updated 25 days ago by Guangchuang Yu1.6k
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Comment: C: Sorting heatmaps by gene expression
... Hi Ryan, it's me again. When I performed `computeMatrixOperation` using the self-constructed matrices, a warning prompted out > chrom, start, end, name, score, strand = region[0:6] ValueError: not > enough values to unpack (expected 6, got 1) I think that there is something wrong during the ...
written 5 weeks ago by chiefcat70
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Comment: C: Sorting heatmaps by gene expression
... Thanks Ryan. Do I need to save the BED6 file as .bed6 when inputting into `computeMatrix` ? ...
written 5 weeks ago by chiefcat70
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Comment: C: Sorting heatmaps by gene expression
... Thanks Ryan. I'm now trying to construct the matrix for FPKM plotting. In parallel, I need to perform the `computeMatrix` for the ChIP-seq. files. I am now creating the bed file for that but want to clarify some concepts. When performing `computeMatrix`, - If a bed6 format is used, isn't it no ` ...
written 5 weeks ago by chiefcat70
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Comment: C: Sorting heatmaps by gene expression
... Hi Ryan, thanks for your suggestion. I've got some questions in regard to the two methods. **1st method (bed file presorted by expression):** - Is there any way that a tabular illustration of the gene sorted (by FPKM) can be put near to the deeptools generated heatmaps (e.g. occupancy data) Examp ...
written 6 weeks ago by chiefcat70
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[How to Save plots in R] DiffBind
... Hi, I'm trying to use a R package for the first time. Does anyone know how to save/ export a plot (e.g. heatmap) in DiffBind? Example: in there example (https://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf) Heatmap was generated by plot(tamoxifen) or ...
R diffbind chip-seq written 6 weeks ago by chiefcat70 • updated 6 weeks ago by Rory Stark320
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Comment: C: Signal desert in ChIP-seq. data? (no signal/ noise in some regions)
... Hi ATPoint, Thanks for your detailed explanation and suggestion. Yes, the total loss-of-signal is really due to masking. So, this is just visualization problem that won't affect the peak-calling, right? ...
written 7 weeks ago by chiefcat70
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Comment: C: Signal desert in ChIP-seq. data? (no signal/ noise in some regions)
... Hi Carlo, After checking the nucleotide sequence in IGV as suggested by ATPoint, I found that the missing of the signal is due to masking. Thanks for your input! ...
written 7 weeks ago by chiefcat70
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Signal desert in ChIP-seq. data? (no signal/ noise in some regions)
... Hi guys, Do you ever see there are some regions doesn't have any signal (not even noise) in ChIP-seq. data? What is the cause/ meaning of this?? Thanks! My case is occurred at genic region, like below (Red box): ![enter image description here][1] [1]: https://i.imgur.com/9ihrdM3.jpg ...
chip-seq written 7 weeks ago by chiefcat70 • updated 7 weeks ago by Carlo Yague3.3k
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Forum: [Please share] How do you keep your NGS data analysis methods/ strategies up to date? (e.g. Data sub-groupping, datasets overlapping, etc.)
... Hi everyone, I am new in analyzing NGS data. Just want to ask how do you guys learn the strategies/ get yourself update in analyzing genome-wide data? (e.g. data sub-groupping, filtering, illustration methods) Although many studies employ genome-wide data analysis, it is impossible to read them al ...
ngs chip-seq forum rna-seq written 8 weeks ago by chiefcat70 • updated 8 weeks ago by Russ150

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