User: jinxinhao1988

gravatar for jinxinhao1988
Reputation:
60
Status:
Trusted
Location:
China/Beijing
Last seen:
3 months ago
Joined:
2 years, 8 months ago
Email:
j************@163.com

I am a new hand in bioinformatics.My postgraduate work focuses on plant transcriptome. And now doing SV, SNP calling work in the disease.

Posts by jinxinhao1988

<prev • 33 results • page 1 of 4 • next >
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Comment: C: Pindel lower the mutation rate in indel calling
... Thank you Kevin for your reply. The main problem is that the pindel wrongly estimated the VAF of indels, so I think that the filteration may not help much. I have tried to adjust the -E parameter, It didn't change much. I have contacted with the author of the software, and he replied that the pinde ...
written 3 months ago by jinxinhao198860
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Pindel lower the mutation rate in indel calling
... Dear all, I have a question with calling indels with Pindel. First I use BWA mem in mapping the reads with hg19 reference with default parameter. Then I use pindel to call indels, since I have the standard answers of my data. The mutation rate of indels are all below the answers. I use 1% and 500 ...
snp pindel written 3 months ago by jinxinhao198860 • updated 3 months ago by biostar4155730k
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Answer: A: How to get SNP annotation with 3-letter amino acid abbreviation?
... update: Actually snpEff can feed back 3-letter Amino acid abbreviation. And the results are quite good. ...
written 4 months ago by jinxinhao198860
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How to use mutation rate to identify a homozygous or heterozygous mutation?
... Dear all, I have a question that we use software to call SNP, and get the mutation rate of each SNP, are there any standards to identify if it is a homozygous mutation? like setting a threshold of 40%-80% is heterozygous mutation, and beyond 80% or beneath 40% is homozygous mutation. If there is a ...
snp written 4 months ago by jinxinhao198860 • updated 4 months ago by biostar4155730k
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Comment: C: How to get SNP annotation with 3-letter amino acid abbreviation?
... Hello,fin, Thank you for your script, It worked for my results. ...
written 5 months ago by jinxinhao198860
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Comment: C: How to get SNP annotation with 3-letter amino acid abbreviation?
... Thank you fin. I will try and feed you results. ...
written 5 months ago by jinxinhao198860
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How to get SNP annotation with 3-letter amino acid abbreviation?
... Dear all, Now we used ANNOVAR to annotate our SNP detected. But the result of ANNOVAR is the single-letter Amino acid abbreviation. It's like this: The results I want is like this: So does anyone knows that which annotation software can feed back this 3-letter amino acid abbreviation? Thanks in ...
annotation snp written 5 months ago by jinxinhao198860
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How to evaluate "control" genes in target sequencing data?
... Hi everyone, I've got a batch of target sequencing data and I want to identify the CNV or LOH in Chr1 and Chr19, besides the chr1 and chr19 region, I also have some target regions which are used to call SNPs. Since my samples are all tumor samples, there is no paired normal sample, so I want to fin ...
cnv tumor written 7 months ago by jinxinhao198860
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Comment: C: KOBAS web server
... Yes, I noticed this problem either. It seems that this has last for several days. Maybe you can write an email to the maintainer of the tool to inquiry the reason. ...
written 7 months ago by jinxinhao198860
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Copynumber calculation problem
... Hi all, I've got a question about copynumber calculation. I used Varscan2 and DNAcopy to call CNV. and got the results as follows: ![This is the outcome of chr20.][1] As we can see that the mean of three logratio valuesis 1.2212. Since the logratio is LOG[(tumor copynumber)/(normal copynumber),2 ...
varscan2 cnv written 8 months ago by jinxinhao198860 • updated 8 months ago by biostar4155730k

Latest awards to jinxinhao1988

Scholar 4 months ago, created an answer that has been accepted. For A: How to get SNP annotation with 3-letter amino acid abbreviation?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For How to identify bowtie2 unique mapping using sam flag value?
Autobiographer 2.2 years ago, has more than 80 characters in the information field of the user's profile.

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