User: Ginsea Chen

gravatar for Ginsea Chen
Ginsea Chen130
Reputation:
130
Status:
Trusted
Location:
Chinese Academy of Tropical Agricultural Sciences, Danzhou, China
Last seen:
1 week ago
Joined:
5 years, 4 months ago
Email:
g*********@hotmail.com

Posts by Ginsea Chen

<prev • 90 results • page 1 of 9 • next >
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Comment: C: Low mapping rate for human NGS PE reads to hs37d5 genome
... Thanks for @ATpoint and @genomax. These samples with low mapping rates have been analyzed, and we observed samples with mapping rate lower than 95% always contained some abnormal SNP/indel variations which around with may soft clip bases like follows. ![enter image description here][1] Now, I am ...
written 4 weeks ago by Ginsea Chen130
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Comment: C: Low mapping rate for human NGS PE reads to hs37d5 genome
... I have mapped all unmapped reads to NCBI nr database and not find any matching record. ...
written 4 weeks ago by Ginsea Chen130
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Comment: C: Low mapping rate for human NGS PE reads to hs37d5 genome
... I have used fastqc to treat all unmapped reads, and I get base sequence quality like:![enter image description here][1] and get base sequence content like:![enter image description here][2] [1]: https://i.ibb.co/3YGH4rK/base-seq-quality.png [2]: https://i.ibb.co/cTDcD3p/base-seq-content.png ...
written 4 weeks ago by Ginsea Chen130
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Comment: C: Low mapping rate for human NGS PE reads to hs37d5 genome
... Please try again, I have fixed it ...
written 4 weeks ago by Ginsea Chen130
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Comment: C: Low mapping rate for human NGS PE reads to hs37d5 genome
... For samples which mapping rate lower than 95%, we will observe much soft clip reads around a SNP or indel variations like supplement figure(https://photos.app.goo.gl/FTxpyvn2qZJDGhnC8 ), So we think the unknown reason which causes low mapping rate may influence the accuracy of variations detecting i ...
written 4 weeks ago by Ginsea Chen130
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Comment: C: Low mapping rate for human NGS PE reads to hs37d5 genome
... I have used cutadapter to cut adapter sequences and used our in house script to filter low-quality reads. I have never used fastqc. Thanks for you suggestion, I will try it. ...
written 4 weeks ago by Ginsea Chen130
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Low mapping rate for human NGS PE reads to hs37d5 genome
... Dear all. I sequenced DNA samples of a human being by using NGS technology and mapping reads (length is 90bp) to the human genome (version:hs37d5). Now I detected so low mapping rate (normal sample is higher than 99%, while my value is 88%). I collected all unmapped reads (243118 reads, flag of bam ...
reads ngs hs37d5 human low mapping rate written 4 weeks ago by Ginsea Chen130
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Answer: A: Access data from very big vcf files in R
... You can extract your target information through following linux shell command: zcat ExAC.r1.sites.vep.vcf.gz | head -n x+ | awk '{print $1 $2}' > target.bed x means the number of the first information line; target.bed is your result file. This is a simple operation, you can contact me (cginsea ...
written 2.2 years ago by Ginsea Chen130
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How to use molecular docking to verify positive selection site
... Dear all. I used PAML to identify four positive selection site and posted this information to a manuscript. A reviewer suggested that I should use some dry or wet experiment method to verify these sites, such as molecular docking. I have none of the experiences to perform molecular docking analyses ...
molecular docking positive selection site written 2.2 years ago by Ginsea Chen130 • updated 2.2 years ago by aka001190
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How to extract primates tree model and placental mammal model from vertebrate model in phyloP46way
... Dear All. In the method part of phyloP46way (https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=cons46way), they said that they extract primates tree model and placental mammal model from the vertebrate model, while this description has no detail methods introduction, such as software or optio ...
phylop46way written 2.4 years ago by Ginsea Chen130 • updated 2.3 years ago by Biostar ♦♦ 20

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