User: ben.kunfang

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ben.kunfang10
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Posts by ben.kunfang

<prev • 30 results • page 1 of 3 • next >
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Comment: C: Convert fastqc.gz file to BED file format
... You should use bowtie2 or bwa to map fq.gz to some reference genome (human:hg38/hg19) first to get the sam file and use bedtools to convert sam file to bed file. ...
written 7 weeks ago by ben.kunfang10
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How to count the paired end reads number in given regions
... Hi, I have a celltype.bwt2pairs.bam file from HiC-Pro. I would like to count the number of the paired reads in given regions, for example, how many paired read on the region chr1:80426-82426 and its mate on the region chr1:75071-77071. Thanks in advance, Kun ...
hi-c paired-end bam hic-pro written 7 weeks ago by ben.kunfang10
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Comment: C: How to deal with Hi-C replicates from different patients' tissue sample?
... Thanks for your information. I will try the diffHiC~ ...
written 9 weeks ago by ben.kunfang10
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How to deal with Hi-C replicates from different patients' tissue sample?
... Hi, I have 8 Hi-C data: 4 of them from primary cancer tissue of four patients and other 4 from drug resistant cancer tissue of other four patients. Now I would like to find the chromatin structure differences between primary cancer and drug resistant cancer. I was wondering if there is need to do s ...
hi-c patient replicates written 9 weeks ago by ben.kunfang10 • updated 9 weeks ago by Gordon Smyth2.0k
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Answer: A: TPM for correlation between genes
... I don't think TPM data works for DESeq2, DESeq2 perform an internal normalization. ...
written 4 months ago by ben.kunfang10
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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 7 months 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 7 months ago by ben.kunfang10 • updated 7 months ago by Istvan Albert ♦♦ 85k
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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 9 months 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 9 months 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 11 months ago by ben.kunfang10

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