User: hxlei613

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hxlei61380
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Bangladesh
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6 days, 21 hours ago
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2 years, 3 months ago
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Posts by hxlei613

<prev • 40 results • page 1 of 4 • next >
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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 3 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 5 months ago by hxlei61380 • updated 5 months ago by Emily_Ensembl14k
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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 8 months ago by hxlei61380 • updated 8 months ago by Devon Ryan74k
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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 8 months ago by hxlei61380 • updated 8 months ago by devenvyas440
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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 9 months ago by hxlei61380 • updated 9 months ago by jotan1.1k
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Comment: C: Bias plot from targeted bisulfite sequencing
... Hi,I wonder how to draw a mbias plot using bwameth ? I cant find the script on github.Thank you very much! ...
written 9 months ago by hxlei61380
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Comment: C: CpG coverage of BS-seq ?
... Hi, I updated my question to make sure I have expressed myself clearly. Thank you very much! ...
written 10 months ago by hxlei61380
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CpG coverage of BS-seq ?
... Hello,I have a question about the CpG coverage of BS-seq. In general many papers would say that how many CpGs are covered by their RRBS experiments. I wonder what is the definition of the CpG. Here is an example: + 5' ---CG---3' - 3' ---GC---5' My question is : Are there two CpGs or just one C ...
bs-seq written 10 months ago by hxlei61380
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DMAP for RRBS generate blank output
... Hello everyone! Lately I've been using DMAP to analyse my RRBS. Trimming(trim_galore), mapping(bismark) all seem fine. DMAP works well with test data supplied by [DMAP][1]. However when I use my raw bam generated by bismark, DMAP doesn't generate any output and there is no error message.I don't know ...
rrbs dmap written 11 months ago by hxlei61380
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Possible bug for bismark when methylation calling ?
... Hi, I'm using bismark for bs-seq mapping and methylation calling. I take a glance at the coverage file generated by *bismark2bedGraph*. However, the result seems strange. Take CpG site of chrM for example (because chrM is the smallest chromosome). The coverage file contains sites that are not CpG si ...
methylation bs-seq bismark written 15 months ago by hxlei61380 • updated 14 months ago by Santosh Anand3.2k

Latest awards to hxlei613

Popular Question 11 weeks ago, created a question with more than 1,000 views. For Questions about BreakDancer
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