User: hxlei613

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hxlei61380
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Bangladesh
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Posts by hxlei613

<prev • 45 results • page 1 of 5 • next >
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Comment: C: What's the difference of FPKM generated by htseq and stringtie?
... That is helpful. However I also find some gene whose counts are not zero in all samples and the fpkm I calculate is not zero (for example the average fpkm of such genes can be 300 or 3000) but fpkm generated by stringtie is zero. What's possible reason for that? ...
written 5 days ago by hxlei61380
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What's the difference of FPKM generated by htseq and stringtie?
... Hi I get FPKM for gene (not transcript) from stringtie by these parameter: -e -G -A. I also use htseq (default parameter )to generate counts matrix for the same gene sets and calculate fpkm using R. The gtf I used in this two method is the same. However the result fpkm is not the same. It seems that ...
htseq fpkm stringtie written 14 days ago by hxlei61380 • updated 14 days ago by Devon Ryan86k
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Question about PCA plot using RPKM/FPKM.
... Hi, after searching for how to draw PCA plot using FPKM, there is still a question confusing me. For example, I have a FPKM matrix (let's say *matrix_sample*) for sample1 sample2 .. sampleN control1, control2 ... controlN (column) and gene1, gene2 ... geneN(row). I want to check if the data have bat ...
fpkm pca rna-seq written 8 weeks ago by hxlei61380 • updated 8 weeks ago by Kevin Blighe33k
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how to detect association between SNP and expression?
... Hi, I want to find the association between SNP and expression in normal CD4+. However I only have 18 samples. If I have hundreds of samples I can do eQTL analysis. What can I do in this situation ? I haven't find any solution yet. Glad for any suggestion. Thanks. ...
expression association snp written 9 weeks ago by hxlei61380 • updated 9 weeks ago by Dhana70
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Are there needs to perform imputation for genotype generated from WGS ?
... I know imputation is usually performed for genotypes from chips. What if these genotypes are from WGS ? It's true that WGS is expensive for a huge population. WHat about your opinions ? ...
wgs imputation written 6 months ago by hxlei61380 • updated 6 months ago by YaGalbi1.4k
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How to infer allele specific expression gene without phasing information?
... Hi, I've read many papers about allele specific expression(ASE). Most of them have phasing data so it is reasonable for them to get allele specific expression genes. For those who don't have phasing information, they just perform test on heter-SNPs but they also get corresponding genes without detai ...
allele specific expression written 14 months ago by hxlei61380
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ensembl transcript id to gene symbol using biomart
... Hi. I am using biomart to convert ensembl transcript id to gene symbol. However there seems to be something wrong. Because in the output there is an ensembl transcript id which has two symbol. Here are my script. > ensembl <- useMart(host="dec2013.archive.ensembl.org", biomart = "ENSEMBL_ ...
R biomart ensembl written 16 months ago by hxlei61380 • updated 16 months ago by Emily_Ensembl16k
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Question about details of the calculation of bisulfite conversion rates.
... Hi! I wonder some details about the calculation of bisulfite conversion rates. 1. It seems that conversion rate can be calculated using all types of C ( CpG, CHH, CHG ) ? 2. How about the coverage of every single C? 5X or 10x ? Is there a threshold ? Another question about CpG methylation rates: ...
bisulfite conversion rates written 19 months ago by hxlei61380 • updated 19 months ago by Devon Ryan86k
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How to call mitochondrial SNP?
... Hello. I have searched this question on biostars already.But I am not satisfied with the result. MitoSeek need a control to call mutation.Well I dont have a control. I have seen many papers said they used GATK but they didnt clearify UnifiedGenotyper or HaplotypeCaller. I also see someone try to use ...
mitochondrial snp written 20 months ago by hxlei61380 • updated 20 months ago by devenvyas520
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(Closed) Heteroplasmy and homoplasmy in mtDNA
... I have read some papers inorder to get a better understanding about heteroplasmy and homoplasmy in mtDNA. But I am still confused about the definition of heteroplasmy and homoplasmy . Could someone please give an easily undertanding explaination ? Thank you very much! ...
mtdna heteroplasmy homoplasmy written 20 months ago by hxlei61380 • updated 20 months ago by jotan1.2k

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