User: Ginsea Chen

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

Posts by Ginsea Chen

<prev • 92 results • page 1 of 10 • next >
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Comment: C: Is structure variations detected in DNA panel sequencing should also be detected
... Thanks for your reply. We used our in house application to detected structure variations in DNA sequencing results (panel capture, FFPE sample with 2-5 years ) and used Arriba to detected structure variations in whole transcriptome results. Some EML4-ALK fusions with high support reads in DNA while ...
written 4 months ago by Ginsea Chen130
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Is structure variations detected in DNA panel sequencing should also be detected in whole transcriptome sequencing
... Dear All. Some EML4-ALK fusion variations were detected in DNA panel sequencing results, while we can't find them in the whole transcriptome sequencing results which produced from the same sample. So, My question is structure variations detected in DNA sequencing results should also exist in whole ...
rna structure variation dna written 4 months ago by Ginsea Chen130 • updated 4 months ago by d-cameron2.2k
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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 9 months 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 9 months 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 9 months 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 9 months 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 9 months 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 9 months 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 9 months 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 3.0 years ago by Ginsea Chen130

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