User: Researcher

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Researcher40
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Posts by Researcher

<prev • 56 results • page 1 of 6 • next >
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Comment: C: Exploring H3K27me3 loss in cancer
... Hi [Kevin][1] Thank you for your reply. I have a follow-up question, will you also suggest to find these pattern only around TSS? [1]: https://www.biostars.org/u/41557/ ...
written 6 days ago by Researcher40
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Comment: C: Defining bivalent promoters with H3K4me3 and H3K27me3 ChIPseq data
... Hi [sikhtechai][1], I am also looking for suggestions for my question where I have H3K27me3 and H3K4me3 data from two different subtypes of a cancer. By any chance did you figure out the answer you were looking for? Would you mind sharing your thoughts and strategy you ended up with? [1]: https ...
written 7 days ago by Researcher40
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Comment: C: Exploring H3K27me3 loss in cancer
... Sure will keep a note. Thanks! Do you have a suggestion for my question? ...
written 8 days ago by Researcher40
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Comment: C: Exploring H3K27me3 loss in cancer
... Hi **[steve][1]**, I want to find out sites that have lost H3K27me3 (repressive) signal but have gained H3K27ac (or any other activation mark) in one cancer subtype compared to other and find out some pattern. But I am a bit confused whether it is recommended to compare the exact coordinates between ...
written 8 days ago by Researcher40
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Comment: C: Exploring H3K27me3 loss in cancer
... Ya I am looking for some suggestion from any of forum, will remove it from there. Thanks for pointing. ...
written 8 days ago by Researcher40
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Comment: A: Exploring H3K27me3 loss in cancer
... I thought so, as I read it somewhere that H3K27ac shares a location with H3K27me3 and often seen interacting with H3K4me3 in bivalent domains. Any suggestion or insight will highly be appreciated. Thanks ...
written 8 days ago by Researcher40
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Comment: A: issue with fastQ reads download from NCBI-SRA database?
... I agree with ATpoint, additionally you can even get fastq file for each read by downloading SRA files which have .sra extension. You can use sra toolkits’s fastq-dump command with its --split-files option for splitting it into 2 fastq. ...
written 8 days ago by Researcher40
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Exploring H3K27me3 loss in cancer
... Hi All, I am looking for some insights for my question interest. I have Chip-Seq data for histone marks from 3 different subtypes of a cancer which have different levels of aggressiveness. I am interested to see if there is any association between the tumor aggressiveness and H3K27me3 loss. Tow ...
h3k27me3 diffbind macs2 chip-seq histone written 9 days ago by Researcher40
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Comment: C: What are the most important filters provided by Mutect2 and how should we order
... Here my concern is I am left with few thousands of sites (~2000) even in a WGS data from human genome, which looks quite weird. I am looking for any suggestions, Is it really ok to have such a few call from WGS data using mutect2? ...
written 14 days ago by Researcher40
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Comment: C: Are MACS2's summit or DiffBind's summit options are recommended for histone mark
... Hi [**@colin**][1], Thanks for explaining it well. But then, what do you think about the DiffBind's summit option, will that help? Hi **[@Rory][2]**, Do you have any suggestions on this? [1]: https://www.biostars.org/u/6733/ [2]: https://www.biostars.org/u/10855/ ...
written 14 days ago by Researcher40

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