User: chengye

gravatar for chengye
chengye10
Reputation:
10
Status:
New User
Location:
China/Shenzhen/BGI
Twitter:
Yeh Chan
Last seen:
6 months, 1 week ago
Joined:
6 months, 4 weeks ago
Email:
c******@genomics.cn

One green-hand in bioinformatics,Graduated from the Southern Medical University in China.

Posts by chengye

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Homologous sequences problematic in RNA-seq
... Actually, not only homologous sequences but also widespread repeats in our genome do have similar problems in data analysis due to the alignment with uncertainty. ...
written 6 months ago by chengye10
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Forum: Homologous sequences problematic in RNA-seq
... As we know ,there exist numerous homologous sequences in our Human genomes. This problem has impeded our process in the downstream analysis of RNA-seq, e.g. in the quantification estimations due to the fact that reads derive from these regions must be aligned to many positions. Some algorithms may d ...
genome forum homology rna-seq written 6 months ago by chengye10 • updated 6 months ago by h.mon27k
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Answer: A: Significance of De Novo Assembly in comparison to Mapping Assembly
... Actually,previously we might tend to use the reference genome if it existed. But now these two strategies are jointly employed to call variations especially Indels or CNVs. You could refer to the GATK HaplotypeCaller methods of reassembly of local activate regions. ...
written 6 months ago by chengye10
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Difference between HC and UG methods
... When I compared the result of HaplotypeCaller and Unifiedgenotyper, I found some locus that only be calling variation by UG. However, the origin bam file and bamout file produced by reassembly both contain this variation(see the figure 1). The number of reads supporting reference and alter allele ar ...
gatk next-gen algorithm sequencing written 6 months ago by chengye10 • updated 5 months ago by Biostar ♦♦ 20
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Comment: C: GATK HaplotypeCaller Problems
... I feel sorry to explain that the command I supplied is just a simple copy from the GATK website while the command I used is below `/ifs4/HST_5B/USERS/cuixiaoli/Software/jdk1.8.0_144/bin/java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_wri ...
written 6 months ago by chengye10
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Comment: C: GATK HaplotypeCaller Problems
... It's one file that GATK4 outputs like 19B0117126-1_gatk4_all.vcf while the prefix is the sample ID. ...
written 6 months ago by chengye10
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GATK HaplotypeCaller Problems
... Recently I used GATK4 to calling variations with the HaplotypeCaller and the bam file that HC produced during reassembly has been required to output using this command guided by GATK instructions. `java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R human_b37_20.fasta -I recalibrated.bam -o hc_v ...
software error gatk next-gen alignment written 6 months ago by chengye10 • updated 5 months ago by Biostar ♦♦ 20

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