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Comment: Filter criteria for variants based on GBS data

Comment: TCGA dataset normalization

Understanding Imputed Genotypes

C: Cox regression survival analysis - using a panel of genes with TCGA

C: Scaling data using Pheatmap

A: Database of HERV integration locations

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Comment: Weird error from BWA and BOWTIE2 by ATpoint 53k

Do you use a job scheduler such as SLURM, if so please add the submission parameters.

Comment: Use BLAST Command Line Applications on combined FASTA files by Michael Dondrup 49k

Sorry I made a mistake, the name of the parameter `qcovs` not qcov and should be a fraction. Could you try again? For an explanation see ht…

Comment: Beagle 5.2 Imputation Issue, understanding output by Matt • 0

The problem is with singleton sites (note the number of markers in your window). The solution is to exclude these scaffolds using the exclu…

Comment: Problem with viewing BAM files in IGV by manfi • 0

Samtools view: ![enter image description here][1] Screenshot for 1 line, it seems like the tracks aren't loaded? ![enter image descript…

Comment: RIP-seq : normalize Input with Immunoprecipitated raw counts or not by ATpoint 53k

I have no experience with RIP-seq but usually in something like ChIP-seq one only uses inputs for peak calling as they are globally differe…

Comment: Quick questions about Alevin and AlevinQC by ATpoint 53k

> When I run AlevinQC why the Number of used reads (which Alevin documentation says are reads that are used for quantification) greater tha…

Comment: Problem with viewing BAM files in IGV by Pierre Lindenbaum 138k

> as verified by inspecting the BAM file with samtools view show us a few lines of "samtools view" and show us the screenshot of IGV for …

Comment: compare two vcf files by 순연 • 0

thank u sir , happy Korean Thanksgiving Day 1) how you want to rank those common rs IDs 선생님이 알려주신 코드를 이용해서 두개의 파일에 중복되는 rsID가 있고 또한 여…

Comment: Doing multiple testing correction before or after GO analysis by dsull ★ 2.3k

Honestly speaking, your gene list is not "statistically robust" (it's arbitrary since you have no sense of the actual false discovery rate)…

Comment: bedtools getfasta concatenating sequences by Juke34 ★ 6.3k

Ok it is because the first command create gene features only and the second remove gene feature if they do not have any sub-feature like mR…

Comment: What does it mean BLASTx in de novo RNAseq analysis? by lieven.sterck 12k

yes, that is very possible indeed. however, running blastx on the 'raw' genomic is somewhat less intuitive to interpret. If you have annot…

Comment: TPM value from DESE2 and significant filterig isssue by ATpoint 53k

Hi, could you please reformat this post using the code `10101` option to highlight code and data?

Comment: desEQ2 eRROR by Nai • 0

res_ddsDE_new has 36,000 rows. When I am using subset(res_ddsDE_new, padj < 0.05 & abs(log2FoldChange) > 1) res_ddsDE_new baseMean log2Fo…

Comment: TCGA dataset normalization by ruby4bioinfo • 0

Thanks Kevin, i got following output str(countData) 'data.frame': 60488 obs. of 183 variables: $ Ensembl_ID : chr "ENSG00000000003…

Comment: Why there are same name with different value in my microarray result? by Aki • 0

Thank you JC! Do you know how to combine these spots as one miRNA? Or do we treat them differently?

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