User: ben.kunfang

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ben.kunfang10
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Posts by ben.kunfang

<prev • 25 results • page 1 of 3 • next >
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Comment: C: Do I have to use index with trans information for RNA-seq alignment by Hisat2?
... Thanks a lot! In this case, I can directly use the pre-built mm10 index for RNA-seq alignment without *trans* in it, right? If you don't mind, can I ask why hisat2 offers the trans and snp index for grcm38 if it can handle the transcriptomic alignment by itself? Thanks again! ...
written 6 days ago by ben.kunfang10
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Do I have to use index with trans information for RNA-seq alignment by Hisat2?
... Hi, I am a newbie in RNA-seq analysis. I would like to use HISAT2 for RNA-seq alignment. In HISAT2 website, I found that pre-built index have *genome_snp_tran* of grcm38 and *genome* of mm10. I was wondering if I could use mm10 *genome* for RNA-seq alignment? If I cannot, I was wondering how can bu ...
rna-seq hisat2 written 6 days ago by ben.kunfang10 • updated 6 days ago by Istvan Albert ♦♦ 83k
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Answer: A: Difference between "peaks" and "hotspots" in Output.type of ENCODE DNase-seq dat
... The "hotspots" files are DNaseI sensitivezones, provided in two file formats (bed broadPeak, and bigBed broadPeak for visualization). "hotspots" are genomic regions enriched for cleavage by DNaseI, corrected to remove false positives. Narrow regions of local maxima from these "hotspots" are called a ...
written 12 weeks ago by ben.kunfang10
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How to get the fine-mapped SNPs associated with risk loci
... Hi, I am a rookie in this field so this might be a silly question, but how can I get the fine-mapped breast cancer risk-associated SNPs? By reading the paper, I have already found the list of 172 risk loci, but I don' t know how to find the SNPs associated with it? Another question is, is one risk ...
fine-mapped gwas snps breast cancer written 12 weeks ago by ben.kunfang10
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Answer: A: macs2 call peak
... I think it is because sequence tech only read the end of the reads, so the actual position of the peak is not the peak of the reading reads. In this case, macs2 will shift a distance to get the real peak position. please check "calling peak" part in this link https://galaxyproject.org/tutorials/chip ...
written 4 months ago by ben.kunfang10
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Comment: C: What's the difference between enrichKEGG and gseKEGG
... Here is what I think, if you know the answer, you could answer the way Iike I answered.It doesn't need to type a lot of words and spend a lot of time. If you don't know the answer, you might giving the wrong books, so what's the point to give the help books? But still, I appreciated you answer my qu ...
written 4 months ago by ben.kunfang10
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Comment: C: What's the difference between enrichKEGG and gseKEGG
... I appreciate h.mon answer my question and I never say h.mon answer is wrong, I just say personally I don't like the way he answer. If you think answer a question by throwing a bunch of books is an appropriate way. That's fine. If you look my answer, don't you think it is more explicit than h.mon's? ...
written 4 months ago by ben.kunfang10
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Comment: C: What's the difference between enrichKEGG and gseKEGG
... Thanks, but I have to say I just don't like to way your answer. Yes, we can learn a lot by reading the help book, but what's the point I ask in the forum..I just want to save a little bit time to get a concise answer. Or otherwise why we need to go to school, we can just study at home by reading all ...
written 5 months ago by ben.kunfang10
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Comment: C: What's the difference between enrichKEGG and gseKEGG
... gseKEGG use the gene set enrichment analysis and enrichKEGG use over-representation test, and GESA doesn't need to run differential gene expression analysis beforehand ...
written 5 months ago by ben.kunfang10
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What's the difference between enrichKEGG and gseKEGG
... Hi, I was wondering what is the difference between enrichKEGG and gseKEGG in R package ClusterProfile. Thanks! ...
clusterprofiler kegg written 5 months ago by ben.kunfang10 • updated 5 months ago by h.mon29k

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