User: boymin2020

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boymin20200
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Posts by boymin2020

<prev • 18 results • page 1 of 2 • next >
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Comment: C: Read length of RNA-seq from HiSeq 2500
... @genomax, thanks for introducing BBMap suite. But it seems I should know the adapter sequence before trim. ...
written 2 days ago by boymin20200
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pancreatic cancer datasets
... Hi, Recently, I have been looking for some pancreatic cancer datasets in order to supplement my research. Of course, TCGA is already done. Just want to know if there are any other datasets including this disease. It will be perfect if it have downloadable GWAS or WES data. Thanks. ...
dataset pancreatic cancer written 13 days ago by boymin20200 • updated 10 days ago by Kevin Blighe17k
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tRNA calling in RNA-seq dataset from a standard sequencing run
... Hi, Recently, I am trying to do tRNA calling in RNA-seq dataset from a standard sequencing run with the goal to obtain their expression abundance. I know some modifications (e.g., methylation) affects the final results. But also want to check if anyone in this community has experience about this ki ...
methylation rna-seq trna written 13 days ago by boymin20200
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Comment: C: Read length of RNA-seq from HiSeq 2500
... Thank for the reply. Could you also tell me how I see the read-though in illumina adapter? ...
written 15 days ago by boymin20200
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Comment: C: Read length of RNA-seq from HiSeq 2500
... Thanks for the reply. Based on what you said, the fragments whose length are less than the specific sequencing length (e.g., 100bp) are not sequenced? ...
written 15 days ago by boymin20200
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Read length of RNA-seq from HiSeq 2500
... Hi, Recently, I received some RNA-seq datasets from our co-operators. I have checked the qualities with FASTQC tool. The distribution of read length just includes 100bp. I want to know what is the sequencing range of fragments? Do the datasets have reads with <100 bp reads. If so, why they have ...
sequence rna-seq written 15 days ago by boymin20200 • updated 15 days ago by genomax46k
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Difference between SNParray genotype dataset and WES genotype dataset
... Hi all, I have handled many genotype datasets from SNP-array dataset or WES dataset. I found the standard PLINk QC methods for GWAS cannot be applied to genotype dataset from WES simply. For example, relatedness check step will screen more outliers. The heterozygous rate scale is smaller. It is kin ...
rnaarray wes genotype gwas written 5 months ago by boymin20200 • updated 5 months ago by Kevin Blighe17k
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Advice required for remove batch effect which perfectly collinear with contrast of interest
... I have merged two RNA-seq datasets from two different batches. The problem is that the sequencing batches are perfectly collinear now with cell type, which means that we are unable to correct for batch effects when computing residuals. Not adjusting for any covariates would risk inducing spurious ...
rna-seq batch effect written 7 months ago by boymin20200 • updated 7 months ago by genomax46k
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Comment: C: Java memory issue in GATK
... That is one kind of situation. But the job had run a long time and all of the nodes show very enough unused memory. ...
written 13 months ago by boymin20200
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Java memory issue in GATK
... I am using HaplotypeCaller of GATK to do variants calling for near 349 WGS human data, which means there are 349 jobs in the cluster. The following is my command. java -Xmx4G \ -Djavaio.tmpdir=$tmp \ -jar $jar \ -T HaplotypeCaller \ -R $ref \ --genotyping_mode DISCOVERY \ ...
haplotypecaller gatk java written 13 months ago by boymin20200 • updated 13 months ago by genomax46k

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