User: Francis

gravatar for Francis
Francis10
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4 days ago
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2 years, 5 months ago
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Posts by Francis

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Comment: C: the peaks of ChIPseq are few
... Thanks. I am suspicious for this, too. I will check the replicates and randomly selected the same reads number for downstream analysis. I will verify the biologically meaningful or other reasons. Thanks for your advice! ...
written 6 months ago by Francis10
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Comment: C: the peaks of ChIPseq are few
... Yes, I hope the change is true, but it is huge. So I am suspicious. Thanks again and I will check the replicates. ...
written 6 months ago by Francis10
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Comment: C: the peaks of ChIPseq are few
... Thanks for your reply. I will read the papers and try to use the deeptools. But as the above: The question is that: I would like to study the k27ac dynamic in the process from A to D. Could it be to compare them directly if they have different peaks through the annotated genes? Thanks. ...
written 6 months ago by Francis10
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Comment: C: the peaks of ChIPseq are few
... Thanks for your reply. Yes, those counts are filtering (quality > 30 and remove duplicated, but not blacklisted regions). I do not use control (or INPUT) bam. The background is OK (maybe) because I can see the clear and same peaks in repeat data. (the relative high of peak is same among differ ...
written 6 months ago by Francis10
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the peaks of ChIPseq are few
... Hi, I would like to study H3K27ac modification in some stages. I have the below bam files and the number is read counts. 113,664,782 A.bam 87,305,342 B.bam 83,029,416 C.bam 49,539,212 D.bam I used MACS2 to call peak: macs2 callpeak -t $input -q 0.05 -f BAM -g hs -B ...
next-gen chip-seq call peak written 6 months ago by Francis10 • updated 6 months ago by Friederike5.1k
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Comment: C: Hi-C contact probability
... Hi, can you solve this problems? I have trouble in this figure. I read the paper about [Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome][1], But I am more confused. So, if you could solve this, could you add a comment? Or how to calculate the frequenc ...
written 6 months ago by Francis10
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Comment: C: R packages error - unable to load shared object
... Thanks for your answer. I am sorry that the reply is late. Yes, it`s a good ideal to creat a new environment for analysis. I uninstalled miniconda and reinstalled again, it works now. Thanks! ...
written 6 months ago by Francis10
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Comment: C: R packages error - unable to load shared object
... I am sorry about the category and thanks for your advice. I learn something from this links, thank you. ...
written 6 months ago by Francis10
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R packages error - unable to load shared object
... I use the conda update the R language and then I require packages but there is a error. > unable to load shared object > '/home/slee_pkuhpc/lustre1/test/software/miniconda2/lib/R/modules//internet.so': > libssl.so.1.0.0: cannot open shared object file: No such file or > ...
R miniconda conda written 6 months ago by Francis10 • updated 6 months ago by zx87548.2k
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How many CPU or MEM does need to run HiC-Pro ?
... Hi, everyone, i am running HiC-Pro to process HiC data to study the interaction frequency of some intar-chr. But the time is too long to finish. i set the CPU of config-hicpro.txt 20 and about 60G mem, i do not know is it suitable. Any ideas will be helpful. Thank you. ...
hic;hic-pro;3d structure; written 17 months ago by Francis10 • updated 17 months ago by genomax71k

Latest awards to Francis

Popular Question 10 months ago, created a question with more than 1,000 views. For Output of featureCounts() is not integer
Popular Question 10 months ago, created a question with more than 1,000 views. For the results of featureCounts do not have `Geneid`
Scholar 2.4 years ago, created an answer that has been accepted. For A: Error: running command '"D:/program files/R-3.3.3/bin/x64/R" --no-site-file --no

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