User: chiefcat

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chiefcat70
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Posts by chiefcat

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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 2 hours 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 2 hours 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 5 hours ago by chiefcat70 • updated 4 hours ago by Carlo Yague3.2k
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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 7 days ago by chiefcat70 • updated 7 days ago by Russ40
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Gene annotation from genomic features
... Hi guys, I've a got basic question regarding gene annotation. What kind of genomic features can be assigned to genes (other than TSS, TTS, exon, intron, enhancer)? Thanks! Kylie ...
annotation chip-seq rna-seq written 8 days ago by chiefcat70
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[Graph plotting] Correlation between gene expression & histone marks (Anyone know how to plot one/ the one like this figure?)
... Hi does anyone know how to plot the figure below or a similar one? Thanks! https://www.nature.com/articles/ncomms15120/figures/3 ![enter image description here][1] [1]: https://i.imgur.com/iYOm1x6.jpg ...
chip-seq rna-seq written 11 days ago by chiefcat70 • updated 10 days ago by Jean-Karim Heriche13k
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Comment: C: ChIP-seq. analysis Tutorial for Dummies
... Thanks Mike! I will read them. Tommy's page seems very informative and details. =] ...
written 11 days ago by chiefcat70
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ChIP-seq. analysis Tutorial for Dummies
... Hi all, Does anyone know is there some material (e.g. books, webpage, etc.) really guides beginners for ChIP-seq. analysis? I'm very struggling with the analysis since I don't have any background in handling NGS data or using command-line tools. However, I need to communicate with my labmates who ...
dummy chip-seq written 11 days ago by chiefcat70 • updated 11 days ago by Gildas Le Corguillé10
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Comment: C: Tools for investigating the correlation of differential gene expression & histon
... Thanks Shoujun, what kind of tools can be used for the visualization of the intersection result? Do you just usually present it using Venn diagram other any other better way which can really show the changes of all genes between two samples? ...
written 11 days ago by chiefcat70
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Comment: C: Tools for investigating the correlation of differential gene expression & histon
... Hi Shoujun, I've just got the Cuffdiff output found the labmate who help me to handle the RNA-seq. data, what kind of corrdinate I should use for the bedtools intersect? Do you have any examples in your hand? Thanks! ...
written 11 days ago by chiefcat70

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