User: CrazyB

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CrazyB210
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Posts by CrazyB

<prev • 57 results • page 1 of 6 • next >
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which exome pipeline to use post PrecisionFDA challenges ?
... As a non-bioinformatician, after PrecisionFDA Truth Challenge and Consistency Challenge, what's the consensus, if any, in terms of exome-seq pipeline to use ? ...
ngs wes written 7 weeks ago by CrazyB210 • updated 6 weeks ago by Charles Warden7.5k
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Comment: C: is there a web-based tool to cross-species compare multiple nucleotide or protei
... Thanks a lot. Both indeed offer the function for batch sequence comparison ! ...
written 10 weeks ago by CrazyB210
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is there a web-based tool to cross-species compare multiple nucleotide or protein sequences for identity and homology in batches
... I have a list of 100 50-bp probe sequences that match 100% to respective human genes. I've searched but failed to find any website that allows me to upload the whole 100 sequences and blast them all to, say, mouse genome. Does anyone know if such an online tool exists ? (I am certain code-based tool ...
alignment homology written 10 weeks ago by CrazyB210 • updated 10 weeks ago by jared.andrews074.3k
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"high" quality RNA but poor RNAseq results
... Wonder if anyone else on this forum has similar experience with high quality RNA, defined by DV200 metrics, but poor RNAseq results, defined by poor concordance of RNAseq results from different RNAseq platforms. The samples in question are extracted RNA from FFPE samples. As RIN values are generall ...
rna-seq written 9 months ago by CrazyB210 • updated 9 months ago by Charles Warden7.5k
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batch effects of RNAseq data from public databases - need to correct or not ?
... CCLE, TCGA, & GTEx have provided RNAseq data but there was very little information available regarding whether batch effects correction is needed when data from different datasets are combined or compared. I found only one publication that addresses the batch effect, as if batch effects per se i ...
rna-seq written 9 months ago by CrazyB210 • updated 9 months ago by cfos4698130
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Are all RPKM/FPKMs in RNAseq "equal" ?
... I am seeking answers to my specific question and general references for this question - My superficial understanding of RPKM is the term is a unit of RNA-seq output and refers to read per kilobase per million read. The calculation takes into account the library size and mRNA length to provide a gen ...
rpkm rna-seq written 10 months ago by CrazyB210 • updated 10 months ago by Charles Warden7.5k
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Comment: C: anyone with experience of RNAseq from FFPE samples on Novaseq vs. that on Hiseq
... @genomax. Thanks for sharing. I will seek input at seqanswers regarding prep kits. ...
written 12 months ago by CrazyB210
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anyone with experience of RNAseq from FFPE samples on Novaseq vs. that on Hiseq
... I was wondering if anyone on this forum has hands-on experience with RNAseq from FFPE samples running on Novaseq vs. Hiseq machines. From the whitepaper, it's clear Novaseq has a bigger capacity to handle more reads. What's not clear to me is how good the performance is for the new library prep kit ...
novaseq rna-seq hiseq written 12 months ago by CrazyB210 • updated 12 months ago by genomax77k
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Comment: C: references for fold-change cutoff
... Our decision tree is as follows - 1. calculate the fold-change with FDR 2. remove all genes that have FDR >=0.05 3. rank the remaining genes based on fold-changes 4. make an arbitrary cutoff of the fold-change - we set it at a low end (1.2-fold) 5. pool all genes that fulfill the FDR and fold-ch ...
written 15 months ago by CrazyB210
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Answer: A: references for fold-change cutoff
... [cancelled by OP - should be a comment not an answer] ...
written 15 months ago by CrazyB210

Latest awards to CrazyB

Great Question 9 months ago, created a question with more than 5,000 views. For What Is Considered A Good Coverage Depth In Exon Capture Seq
Popular Question 9 months ago, created a question with more than 1,000 views. For a question about some "basic numbers" for rna-seq experiments
Popular Question 11 months ago, created a question with more than 1,000 views. For a question about some "basic numbers" for rna-seq experiments
Great Question 15 months ago, created a question with more than 5,000 views. For Negative B-Statistic Values In Limma/Microarray Differential Expression
Popular Question 2.4 years ago, created a question with more than 1,000 views. For is there a value of ranking genes based on p-value in RNA-seq data
Popular Question 2.4 years ago, created a question with more than 1,000 views. For a question about some "basic numbers" for rna-seq experiments
Popular Question 2.4 years ago, created a question with more than 1,000 views. For my VCF file was said to contain no header/meta data when using vcftools
Popular Question 2.4 years ago, created a question with more than 1,000 views. For how to find SNP positions (for non-bioinformaticians)
Popular Question 2.4 years ago, created a question with more than 1,000 views. For how to add pedigree info into VCF
Popular Question 3.3 years ago, created a question with more than 1,000 views. For convert text file to VCF file ?
Good Question 3.3 years ago, asked a question that was upvoted at least 5 times. For What Is Considered A Good Coverage Depth In Exon Capture Seq
Popular Question 3.3 years ago, created a question with more than 1,000 views. For a question about some "basic numbers" for rna-seq experiments
Popular Question 3.3 years ago, created a question with more than 1,000 views. For how to find SNP positions (for non-bioinformaticians)
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Multiplex In Exome Seq And "Customized/Capture" Seq Kits
Popular Question 3.5 years ago, created a question with more than 1,000 views. For What Is Considered A Good Coverage Depth In Exon Capture Seq
Popular Question 3.5 years ago, created a question with more than 1,000 views. For convert text file to VCF file ?
Epic Question 3.8 years ago, created a question with more than 10,000 views. For convert text file to VCF file ?
Popular Question 3.8 years ago, created a question with more than 1,000 views. For convert text file to VCF file ?
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Multiplex In Exome Seq And "Customized/Capture" Seq Kits
Popular Question 3.8 years ago, created a question with more than 1,000 views. For What Is Considered A Good Coverage Depth In Exon Capture Seq
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Multiplex In Exome Seq And "Customized/Capture" Seq Kits
Great Question 4.3 years ago, created a question with more than 5,000 views. For convert text file to VCF file ?

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