User: camelbbs

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camelbbs670
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Posts by camelbbs

<prev • 179 results • page 2 of 18 • next >
8
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Number of reads in one gene affect the differential expression analysis?
... Hi all, I recently calculate the differential expressed genes from RNASeq data by DESeq. One question is bothering me. When we checked the number of reads in every gene we annotated, we found some genes have huge number of reads, compare to total reads, such as: sample s-664561 s-665905 s-65 ...
rnaseq counts deseq deg rna-seq written 3.6 years ago by camelbbs670 • updated 3.6 years ago by i.sudbery7.3k
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Comment: C: Truncate RNASeq data to get similar abundance
... I modified my question, could you take a look again, Thanks. ...
written 3.6 years ago by camelbbs670
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Comment: C: Truncate RNASeq data to get similar abundance
... Thanks, I just write the number for example. Actually I know the normalization process like DESeq. Asking this question because we found the sum of RPKM in each samples are very different. We speculate the reason is sequencing abundance are different. ...
written 3.6 years ago by camelbbs670
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Truncate RNASeq data to get similar abundance
... Hi, We did RNA sequencing in 6 samples and got the results that the total reads number in those 6 samples were very different. For example: sampleA1 sampleA2 sampleA3 sampleB1 sampleB2 sampleB3 150000 160000 180000 250000 260000 250000 Do we need to truncate the same number o ...
rnaseq written 3.6 years ago by camelbbs670
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Do I need to consider strand information in searching microRNA binding sites ?
... Hi all, I want to ask when we extract genomic sequences to predict the microRNA binding sites, do we need to consider the strand information for it? I know the sequences from plus and minus strand are complementary. So which strand I can use for the prediction of microRNA binding sites, or it is no ...
microrna written 4.0 years ago by camelbbs670
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Retrieve RNA-protein binding sites from CLIP-Seq
... Hi all, We want to map the possbile RNA-protein binding (RBP) sites to our predicted transcripts. And after reading literature, we find some works extracting RNA-protein binding sites from Clip-seq data. We want to ask if there is a collection of RBP sites from CLIP-seq in some databases? And if th ...
clip-seq rna protein binding written 4.1 years ago by camelbbs670 • updated 4.1 years ago by lsp03yjh800
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Extract sequences from local genome file by coordinates
... Hi all, I want to ask if there is a bioperl module can extract sequences by coordinates (chr1:12321321-12321921) from local genome file (eg. hg19.genome.fa). We can do that using 'bedtools getfasta', but still want to know if bioperl module can do that? Thanks, Camel ...
sequence bioperl coordinates written 4.1 years ago by camelbbs670 • updated 4.1 years ago by mastal5112.0k
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sample with no replicates using GSEA
... Hi all, I want to ask a question about using GSEA. I only have two samples with no replicates. So I found I can only use Gene_set (not the phenotype) for the permutation type. My question is: Can the result from this option also give us the differentially enriched pathways between the two samples? ...
array gene gsea rna-seq sequencing written 4.5 years ago by camelbbs670
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Why some SNP databases don't contain the strand information
... Hi all, While I checked the database such as ClinVar and COSMIC, I didn't find the strand information (+ or -) for their SNP sites. But the dbSNP database such as SNP142 contains the strand information. So if there is no strand info, how I can know the SNP is located in plus or minus strand? Does t ...
snp strand written 4.6 years ago by camelbbs670 • updated 4.6 years ago by Pablo1.9k
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SNP database in heart development or disorder
... Hi all, I want to ask where I can find the SNP database associated to heart development and disease. Does the clinVar include the information about this. Thanks a lot for any suggestions. Cam  ...
snp development heart written 4.7 years ago by camelbbs670 • updated 3.2 years ago by milosn10

Latest awards to camelbbs

Popular Question 12 months ago, created a question with more than 1,000 views. For sample with no replicates using GSEA
Popular Question 12 months ago, created a question with more than 1,000 views. For Extract sequences from local genome file by coordinates
Popular Question 13 months ago, created a question with more than 1,000 views. For Extract sequences from local genome file by coordinates
Great Question 13 months ago, created a question with more than 5,000 views. For How To Use Tophat With Strand Specifc
Great Question 14 months ago, created a question with more than 5,000 views. For Problems Using Htseq-Count And Samtools When Processing Rna-Seq Data
Popular Question 14 months ago, created a question with more than 1,000 views. For Extract sequences from local genome file by coordinates
Great Question 14 months ago, created a question with more than 5,000 views. For How To Use Tophat With Strand Specifc
Student 15 months ago, asked a question with at least 3 up-votes. For Are There Publicly Available Rna-Seq Datasets From Human Adult Pancreas And Stomach?
Popular Question 17 months ago, created a question with more than 1,000 views. For Extract sequences from local genome file by coordinates
Popular Question 20 months ago, created a question with more than 1,000 views. For Extract sequences from local genome file by coordinates
Popular Question 20 months ago, created a question with more than 1,000 views. For a question about sharing the ucsc custom track to other people
Popular Question 20 months ago, created a question with more than 1,000 views. For Memory For Igv Browser
Popular Question 22 months ago, created a question with more than 1,000 views. For How to find the SNP in promoter regions
Great Question 2.7 years ago, created a question with more than 5,000 views. For Rna-Seq Data In Public Database
Great Question 2.7 years ago, created a question with more than 5,000 views. For Deseq Handle Samples Without Replicates
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Any Database For Cds-Located Mirna Target Sites
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Can I Use Tophat To Align Exome Seq
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Memory For Igv Browser
Popular Question 2.7 years ago, created a question with more than 1,000 views. For How to find the SNP in promoter regions
Great Question 2.7 years ago, created a question with more than 5,000 views. For Normalization Method In Comparing Differential Gene Expression
Great Question 2.7 years ago, created a question with more than 5,000 views. For Draw Heatmap Or Do Pca Analysis With Raw Read Counts?
Student 2.7 years ago, asked a question with at least 3 up-votes. For Are There Publicly Available Rna-Seq Datasets From Human Adult Pancreas And Stomach?
Great Question 2.7 years ago, created a question with more than 5,000 views. For How To Merge Isoforms For A Gene
Great Question 2.8 years ago, created a question with more than 5,000 views. For Rna-Seq Data In Public Database

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