User: boymin2020

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boymin202010
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Posts by boymin2020

<prev • 21 results • page 1 of 3 • next >
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DE heatmap before or after limma adjustment
... Hi, I have a proteomics data from MaxQuant software. According to the manual, the data has been normalized by the MaxQuant internal method. After cleanup, QC and imputation (**imputation data**), I have done the adjustment with limma for AOD, Sex and PMI (**residual data**). In the next step, I wa ...
de heapmap limma written 2 days ago by boymin202010
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Comment: C: MaxQuant LFQ data cleanup
... Thanks for your so fast answer. Moreover, could you tell me the meanings of "MS/MS count" and "reverse" columns in the output of MaxQuant? ...
written 4 days ago by boymin202010
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MaxQuant LFQ data cleanup
... Hi all, I am new to the proteomics data. A little confused about the LFQ data from MaxQuant software. Take some rows as examples **tr|A0A087X106|A0A087X106_HUMAN;sp|O43790|KRT86_HUMAN;CON__O43790;sp|Q14533|KRT81_HUMAN;CON__Q14533** , what is the meaning of "tr" and "sp"? In addition, I have been r ...
maxquant written 4 days ago by boymin202010 • updated 4 days ago by Devon Ryan81k
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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 3 months ago by boymin202010
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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 3 months ago by boymin202010 • updated 3 months ago by Kevin Blighe24k
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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 3 months ago by boymin202010
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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 3 months ago by boymin202010
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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 3 months ago by boymin202010
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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 3 months ago by boymin202010 • updated 3 months ago by genomax52k
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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 8 months ago by boymin202010 • updated 8 months ago by Kevin Blighe24k

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