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1,000 results • Page 2 of 20
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3
votes
2
replies
5.9k
views
Hypergeometric test of gene set enrichment - Calculate P-value for multiple gene sets in one script?
next-gen R GO
updated 9 months ago by 37k • written 8.0 years ago by ▴ 20
2
votes
5
replies
5.8k
views
How to normalize gene expression values for finding similar genes
gene RNA-Seq
updated 6 months ago by 37k • written 7.8 years ago by ▴ 10
2
votes
1
reply
5.8k
views
BEDgraph to BED/bam
bed
updated 3 months ago by 37k • written 7.4 years ago by ▴ 60
0
votes
1
reply
5.8k
views
SNP and gene density along the chromosomes plots
gene-density ggplot2 R SNP
updated 8 months ago by 37k • written 7.3 years ago by ▴ 430
1
vote
1
reply
5.8k
views
how is the output of bcftools stats calculated?
bcftools
updated 4 months ago by 37k • written 7.4 years ago by ▴ 10
4
votes
3
replies
5.8k
views
PLINK2 association study using covariate regression model
SNP plink software-error genome
updated 8 months ago by 37k • written 7.8 years ago by ▴ 20
1
vote
6
replies
5.8k
views
bedGRAPH files from MACS2 ChIP-seq analysis don't reflect peaks called in peak.xls file
ChIP-Seq
updated 4 months ago by 37k • written 7.3 years ago by ▴ 460
6
votes
7
replies
5.8k
views
best alignment tool for Ion Torrent data
chloroplast genome iontorrent
updated 5 months ago by 37k • written 7.2 years ago by ★ 2.3k
2
votes
1
reply
5.8k
views
Reads, Cluster Numbers, Study Design Comparison
cluster-number Read
updated 6 months ago by 37k • written 7.0 years ago by ▴ 10
0
votes
1
reply
5.7k
views
PLINK: Unrecognized flag '--list-duplicate-vars'
IBD BEAGLE PLINK
updated 9 months ago by 37k • written 8.0 years ago by ▴ 580
1
vote
1
reply
5.7k
views
different color for highlighting genes in Manhattan plot in qqman
R genome
updated 4 months ago by 37k • written 7.4 years ago by ▴ 40
3
votes
4
replies
5.6k
views
HTSeq-count, problem in handling PE data
RNA-Seq HTSeq
updated 5 months ago by 37k • written 7.1 years ago by • 0
1
vote
1
reply
5.6k
views
Error: expecting string instruction after `rep' after typing in "make"
kmergenie
updated 5 months ago by 37k • written 7.3 years ago by • 0
3
votes
6
replies
5.6k
views
concordant pair alignment rate is too low
RNA-Seq sequencing alignment
updated 6 months ago by 37k • written 7.0 years ago by ★ 4.1k
1
vote
9
replies
5.6k
views
downloading nt databases - cannot extract them all?
NCBI blast nt BLAST-plus database
updated 8 months ago by 37k • written 7.9 years ago by ▴ 10
0
votes
3
replies
5.6k
views
Setting dimensions of barplot area in R (for STRUCTURE-like plot)
R
updated 3 months ago by 37k • written 7.5 years ago by ▴ 720
1
vote
5
replies
5.6k
views
What is mutation calling in exome sequencing?
Exome Mutation-calling SNP-calling Variant-calling
updated 5 months ago by 37k • written 7.1 years ago by ▴ 350
1
vote
1
reply
5.5k
views
vcf SNP file minor allele frequency filter?
vcf minor-allele SNP vcftools
updated 3 months ago by 37k • written 7.5 years ago by ▴ 130
3
votes
6
replies
5.5k
views
Undefined References From Boost When Installing Bam-Readcount
bam-readcount
updated 6 months ago by 37k • written 9.0 years ago by ▴ 10
5
votes
3
replies
5.5k
views
GATK "We encountered a non-standard non-IUPAC base in the provided reference: '13"
GATK
updated 5 months ago by 37k • written 7.3 years ago by ▴ 20
1
vote
3
replies
5.5k
views
spades; Failed to align paired reads
Assembly
updated 6 months ago by 37k • written 7.0 years ago by ▴ 10
1
vote
4
replies
5.5k
views
Bowtie mismatch settings
bowtie mismatch
updated 11 months ago by 37k • written 8.2 years ago by ★ 1.4k
1
vote
5
replies
5.5k
views
Converting text format Mass spectrometry data to mzXML?
mass spectrometry data formats mzXNL ASCII
updated 7 weeks ago by 37k • written 7.6 years ago by • 0
5
votes
4
replies
5.5k
views
HGNC gene symbols
gene ensembl hgnc
updated 5 months ago by 37k • written 7.1 years ago by ▴ 20
1
vote
8
replies
5.3k
views
Plotting different gene ontology categories in a barplot
HI Gene ontology R
updated 6 months ago by 11k • written 24 months ago by • 0
2
votes
0
replies
5.3k
views
Kraken output to Krona Tools: What can be selected as magnitude
Kraken magnitude Krona
updated 9 months ago by 37k • written 8.0 years ago by ▴ 360
9
votes
1
reply
5.3k
views
Why does MACS2 report multiple records for the same peak region?
ChIP-Seq macs macs2
updated 5 months ago by 37k • written 7.3 years ago by ★ 3.4k
0
votes
17
replies
5.3k
views
7 follow
EXITING: because of fatal INPUT file error: could not open read file
mapping genome fastq STAR
updated 10 months ago by • 0 • written 2.0 years ago by • 0
1
vote
1
reply
5.3k
views
GtfToGenePred errors in converting GTF files.
software-error
updated 6 weeks ago by 37k • written 7.6 years ago by ▴ 100
1
vote
7
replies
5.3k
views
extract sequences ID from a fasta file
extract sequencesID
updated 8 months ago by 37k • written 7.9 years ago by ▴ 230
1
vote
7
replies
5.3k
views
Converter for GFF file downloaded from NCBI to GTF
annotation gff gtf eval
updated 6 months ago by 37k • written 7.0 years ago by ▴ 20
3
votes
3
replies
5.3k
views
R - Merge 2 network with different color nodes
merge R networks
updated 4 months ago by 37k • written 7.3 years ago by ▴ 270
1
vote
0
replies
5.2k
views
ANNOVAR vs VEP
SNP
updated 8 months ago by 37k • written 7.9 years ago by ▴ 600
3
votes
4
replies
5.2k
views
How to convert Affymetrix SNP IDs to dbSNP rs SNP names
PLINK SNP genome Affymetrix
updated 5 months ago by 37k • written 7.3 years ago by ▴ 20
1
vote
0
replies
5.2k
views
additive and multiplicative genetic models in logistic regression
SNP
updated 5 months ago by 37k • written 7.3 years ago by ▴ 10
9
votes
4
replies
5.2k
views
How to analyse normalized read count?
RNA-Seq R
updated 25 days ago by 37k • written 7.7 years ago by ▴ 150
1
vote
6
replies
5.2k
views
output SAM file from STAR aligner looks incomplete
DNAseq alignment aligner STAR
updated 5 months ago by 37k • written 7.2 years ago by ▴ 90
2
votes
1
reply
5.2k
views
WGCNA - problems picking a suitable power
RNA-Seq pickSoftThreshold WGCNA power
updated 6 months ago by 37k • written 7.0 years ago by ▴ 50
5
votes
1
reply
5.1k
views
Generating Gencode TSS file
gencode tss
updated 5 months ago by 37k • written 7.2 years ago by ▴ 210
3
votes
4
replies
5.1k
views
23andme: Convert Human Assembly Build 36 to Build 37
snp genome Liftover bed format
updated 11 months ago by 37k • written 8.2 years ago by ▴ 10
3
votes
1
reply
5.1k
views
Calculating Watterson's Theta and Tajima's Pi from NGS (bam file)
NGS theta pi bam SNP
updated 9 months ago by 37k • written 8.0 years ago by ★ 2.6k
1
vote
4
replies
5.1k
views
Diffbind bioconductor, peaks overlapping
ChIP-Seq diffbind bioconductor
updated 4 months ago by 37k • written 8.4 years ago by ▴ 80
0
votes
4
replies
5.1k
views
MiSeq Analysis Beginner: First steps after getting MiSeq paired end data
reference-genome demultiplexing Assembly MiSeq
updated 9 weeks ago by 37k • written 7.5 years ago by • 0
4
votes
3
replies
5.1k
views
Comparing 2 gene lists
gene
updated 7 months ago by 37k • written 7.8 years ago by ▴ 40
0
votes
0
replies
5.1k
views
Query deleterious score of SNP mutation for various prediction methods with UniProt ID and mutation position
SNP
updated 4 weeks ago by 37k • written 7.6 years ago by ▴ 130
0
votes
0
replies
5.1k
views
QD value from GATK in joint VCF
VCF QD GATK
updated 9 months ago by 37k • written 8.0 years ago by • 0
1
vote
2
replies
5.1k
views
Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
vcf Snpeff annotation
updated 6 months ago by 37k • written 7.1 years ago by ▴ 500
0
votes
9
replies
5.0k
views
PLINK does not uncompress GZ file automatically, why?
plink gz SNP
updated 3 months ago by 37k • written 7.5 years ago by • 0
1
vote
9
replies
5.0k
views
SCTransform prior or after merging samples into one object?
Seurat scRNAseq merging samples
updated 10 months ago by ▴ 690 • written 2.3 years ago by • 0
4
votes
11
replies
5.0k
views
Correct way to calculate VAF (Variant allele fraction) from a VCF file
VCF snp
5 months ago by prasundutta87 ▴ 640
1,000 results • Page 2 of 20
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Recent Replies
Answer: how to do a reliable single cell sequencing analysis? by ATpoint 68k
The usual approach for starters would be to follow guided and well-accepted tutorials. That would (incomplete list) be: - The Biocon…
Answer: a problem with getBM by sanaz • 0
head(ensembl_ids) X baseMean log2FoldChange lfcSE stat pvalue padj 1 ENSG00000000938.13 1344.2587 2.107…
Answer: Recommendations needed for a tool for comparative gene set enrichment analyses v by fuellen ▴ 20
Hello and Thanks! OK, I should have written "The gene lists I have prepared" instead of "The DEG lists I have prepared". In any case, is …
Comment: a problem with getBM by Mike Smith ★ 1.9k
Can you update your post to show some examples of what's in your `ensembl_ids` object? Perhaps the contents of `head(ensembl_ids)`. It's …
Answer: trainGlimmerHMM Error while training a genome by congliu37 • 0
Hello, I got the same error using ~20,000 genes for training and it was solved by reducing training gene set. I assume GlimmerHMM was no…
Comment: How to Calulate Allele Frequency from a VCF File? by Jeremy Leipzig 21k
That's correct. You don't have biallelic alleles in mitochondria, so you can use either the Allele depth (AD) or depth of coverage (DP) for…
Comment: How to calculate tumor mutation burden (TMB)? by Fabio Marroni ★ 2.9k
I just published a [post][1] on my blog, in which I include a simple R function for computing TMB. Try to see if that helps. I followed the…
Comment: Gene Set Enrichment Analysis, pathway, metabolism by Rob ▴ 160
Thank you FrankStarling, ATpoint, jv, these were so helpful.
Comment: translate CDS to prot formatted with nt nubers by Pierre Lindenbaum 152k
> with nucleotide numbers and DNA/prot aligned line by line what does it mean ? Create a Minimal, Reproducible Example to enable others t…
Comment: How to translate CDS to an amino acid sequence by vvasta • 0
I tried several of the online DNA translation tools but have not found one that would output DNA/prot alignment with nucleotide number w…
Comment: How possible deadlocks are there while migrating from MYISAM to InnoDb? by Pierre Lindenbaum 152k
but you already knew it. https://www.biostars.org/p/9551097/#9551098
Comment: How possible deadlocks are there while migrating from MYISAM to InnoDb? by Pierre Lindenbaum 152k
your question is not related to bioinformatics. Ask stackoverflow.com.
Comment: Statistical test for checking cis regulation? by Fabio Marroni ★ 2.9k
Hi lumos. It is not very clear to me what kind of information are you using for the test and how are you measuring cis-regulation. Are you …
Comment: Error 134 while aligning using hisat2 by Fabio Marroni ★ 2.9k
Other instances of the same error were indeed related to disk [space][1]. Can you post the output of the command: `df -h /bams/`? Another p…
Comment: **Error: unable to open file or unable to determine types for file** by Pierre Lindenbaum 152k
``` Please ensure that your file is TAB delimited (e.g., cat -t FILE). - Also ensure that your file has integer chromosome coordinates in t…
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