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711 results • Page
3 of 15
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Votes
Replies
3
votes
3
replies
260
views
getting exon coordinates
genomics
updated 5 days ago by
Ram
44k • written 5 days ago by
Xbox_27
• 0
3
votes
2
replies
332
views
p-value and Boneferroni adjusted p-value the same in R
Bonferroni
R
Statistics
p-value
Fisher
29 days ago by
kristiewyleung
• 0
3
votes
3
replies
390
views
What analysis suitable to identify similarly expressed genes between two samples (treated vs untreated). Contrary to DGE analysis,
Gene-Expression
RNA
NOISeq
DGE
updated 18 days ago by
ATpoint
82k • written 19 days ago by
alifafiq1
• 0
3
votes
1
reply
231
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair
samtools
alignment
updated 8 days ago by
aw7
▴ 300 • written 13 days ago by
Zeng Hao
▴ 40
3
votes
6
replies
2.0k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 25 days ago by
Ram
44k • written 2.4 years ago by
SYOSY
▴ 10
3
votes
4
replies
4.0k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 13 days ago by
chloek88
• 0 • written 5.6 years ago by
Philipp Bayer
8.5k
3
votes
8
replies
739
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core
16S
amplicon
dada2
ampliseq
updated 15 days ago by
Chris Dean
▴ 410 • written 19 days ago by
sovrappensiero
▴ 100
3
votes
4
replies
769
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
29 days ago by
rahu
• 0
3
votes
5
replies
360
views
Generating mpileup file using samtools
mpileup
samtools
updated 18 days ago by
Joe
21k • written 18 days ago by
Ruqaiya
• 0
3
votes
7
replies
431
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
22 days ago by
Sergio A.S.
• 0
3
votes
3
replies
379
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 25 days ago by
GenoMax
142k • written 25 days ago by
sapuizait
▴ 10
3
votes
5
replies
421
views
Super ehancers
enhancers
updated 7 hours ago by
jared.andrews07
★ 17k • written 19 days ago by
Oburah
• 0
3
votes
2
replies
389
views
what is the purpose of indexing the reference genome (Kallisto)
indexing
Kallisto
updated 25 days ago by
dsull
★ 6.0k • written 25 days ago by
Aaliya
▴ 10
3
votes
2
replies
433
views
Extract protein sequence
fasta
alignment
blast
21 days ago by
anna
▴ 20
3
votes
5
replies
428
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
12 hours ago by
beantkapoor16
▴ 10
3
votes
3
replies
294
views
what is another word for a BLAST "hit"?
blast
alignment
11 days ago by
dec986
▴ 380
3
votes
4
replies
429
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
26 days ago by
QX
• 0
3
votes
3
replies
2.5k
views
How to make a TSS enrichment plot in ATAC-seq analysis?
ATAC
updated 26 days ago by
sp
• 0 • written 22 months ago by
Dan
▴ 180
3
votes
4
replies
494
views
Design matrix Differential expression analysis
RNA-seq
Differential-expression
updated 15 days ago by
Gordon Smyth
★ 7.2k • written 18 days ago by
SHN
▴ 40
3
votes
5
replies
425
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
18 days ago by
Maverick
▴ 10
3
votes
8
replies
194
views
Problem in getting geo file through GEOQUERY
file
download
Geo
3 hours ago by
anasjamshed
▴ 120
3
votes
6
replies
537
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 9 days ago by
Pine
▴ 20 • written 16 days ago by
snajafy
• 0
3
votes
5
replies
366
views
Per base sequence content error in RNAseq analysis
RNA-seq
analysis
updated 29 days ago by
GenoMax
142k • written 29 days ago by
ahmad.sajad4541
• 0
3
votes
8
replies
644
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
15 days ago by
Qroid
▴ 40
2
votes
3
replies
345
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 18 days ago by
dthorbur
★ 2.0k • written 18 days ago by
Vijith
▴ 30
2
votes
2
replies
340
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 27 days ago by
Ram
44k • written 28 days ago by
v.berriosfarias
▴ 140
2
votes
3
replies
1.1k
views
Is it possible to run CibersortX with a very small number of samples?
cibersortx
updated 8 hours ago by
finch
• 0 • written 19 months ago by
Aspire
▴ 330
2
votes
3
replies
1.0k
views
Method to detect genome doubling
CNV
genome doubling
updated 29 days ago by
LauferVA
4.2k • written 4.5 years ago by
CY
▴ 750
2
votes
0
replies
188
views
Tool:
Sequence alignment on split read event such as inversion, duplication and complex nested events.
minimap
alignment
NGMLR
2 days ago by
micah
▴ 30
2
votes
2
replies
211
views
Is therer any suggestions on mapping rate of WGBS data?
mapping
read
alignment
WGBS
13 days ago by
Zeng Jingyu
▴ 60
2
votes
5
replies
292
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 7 days ago by
Philipp Bayer
8.5k • written 8 days ago by
林明德
• 0
2
votes
2
replies
213
views
genome finishing
finishing
genome
updated 6 days ago by
nd48
▴ 30 • written 6 days ago by
trezini
• 0
2
votes
2
replies
260
views
Raw counts using stringtie
stringtie
RNA-seq
updated 18 days ago by
GenoMax
142k • written 18 days ago by
ahmad.sajad4541
• 0
2
votes
14
replies
3.0k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 7 days ago by
Anitha
• 0 • written 4.9 years ago by
ww22runner
▴ 60
2
votes
3
replies
265
views
ggrepel function: geom_text_repel()
ggplot2
ggrepel
R
updated 5 days ago by
Ram
44k • written 6 days ago by
sooni
▴ 20
2
votes
4
replies
2.8k
views
When to use .vcf or .gvcf files from GATK HaplotypeCaller?
indel
gatk
calling
snp
variant
updated 22 days ago by
Medhat
9.7k • written 2.0 years ago by
Vitor1
▴ 120
2
votes
2
replies
214
views
Genome Visualization Tools
bacterial
genome
updated 7 days ago by
GenoMax
142k • written 7 days ago by
dlera.lozano
▴ 10
2
votes
5
replies
524
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 7 days ago by
Ram
44k • written 13 days ago by
Prawesh
• 0
2
votes
4
replies
315
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
6 days ago by
Esraa
• 0
2
votes
2
replies
294
views
HaplotypeCaller - only SNPs
HaplotypeCaller
GATK
updated 27 days ago by
analyst
▴ 50 • written 28 days ago by
lorena9132
▴ 10
2
votes
10
replies
1.1k
views
HGVS Nomenclature of Multiple Indels found in Cis
Nomenclature
HGVS
updated 1 day ago by
Ram
44k • written 5 months ago by
LauferVA
4.2k
2
votes
5
replies
562
views
Marking duplicates using UMIs
Deduplication
UMI
updated 29 days ago by
i.sudbery
19k • written 4 weeks ago by
Lipika
• 0
2
votes
11
replies
773
views
DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts in whole blood: is it normal to always get NS?
rstudio
DEG
limma
4 days ago by
egascon
• 0
2
votes
6
replies
1.9k
views
How can you *consistently* download BioProject IDs from NCBI's BioSample database using Entrez Direct?
XML
ncbi
entrez-direct
updated 6 days ago by
Ram
44k • written 3.9 years ago by
millere
• 0
2
votes
4
replies
297
views
Where to get the following bed file?
WES
bed
reference
file
updated 15 days ago by
GenoMax
142k • written 15 days ago by
wyuan37
• 0
2
votes
5
replies
2.6k
views
identifying transgene insertion site in WGS
WGS
insertion site
trangene
de-novo
soap
updated 13 days ago by
Cameron.walker9900
• 0 • written 5.1 years ago by
Assa Yeroslaviz
★ 1.8k
2
votes
7
replies
1.4k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq
Salmon
Isoseq
updated 23 days ago by
Gordon Smyth
★ 7.2k • written 8 months ago by
Calum
▴ 10
2
votes
3
replies
299
views
error in fun(x((i)), ...) : only defined on a data frame with all numeric alike variables
studio
Cibersort
R
8 days ago by
Azra
▴ 10
2
votes
3
replies
872
views
Issues with Mixture file when using CIBERSORTx
Deconvolution
CIBERSORTx
updated 17 days ago by
vjanve
• 0 • written 7 months ago by
mateomejias
• 0
2
votes
1
reply
162
views
java out of memory error through beagle for imutation
beagle
java.out.of.memory
imputation
13 days ago by
analyst
▴ 50
711 results • Page
3 of 15
Recent Votes
GO analysis: Different results EnrichGO vs ShinyGO
Comment: NGS forensics: how to know if data is fabricated
T2T-CHM13 "complete" human genome gff/gtf annotation file
Answer: T2T-CHM13 "complete" human genome gff/gtf annotation file
Comment: Problem in getting geo file through GEOQUERY
Answer: Problem in getting geo file through GEOQUERY
Comment: SnpEff and Snpsift
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Recent Replies
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
▴ 10
Hi Alex, I'm sorry if I wasn't initially clear! The question hasn't changed; I had written in this post that I wanted all pairwise combinat…
Comment: BiomartException: Query ERROR for existing dataset in BioMart
by
Nyksubuz
▴ 20
Could share some examples for gene_ids?
Comment: Problem in getting geo file through GEOQUERY
by
anasjamshed
▴ 120
yeah but i am unable to find the link of GPL6244.soft.gz
Comment: Problem in getting geo file through GEOQUERY
by
ATpoint
82k
> Can you send me ftp link so I can download that soft file manually? Please find this link on your own by browsing the respective GEO ent…
Comment: Problem in getting geo file through GEOQUERY
by
anasjamshed
▴ 120
Thanks . I have downloaded all other files but just have problem in Error in downloadFile(myurl, destfile, mode = mode, quiet = TRUE)…
Answer: Problem in getting geo file through GEOQUERY
by
ATpoint
82k
Code runs for me and finishes in seconds. Maybe some poor internet connection on your end. Just set the timeout to 9999999 and retry. If th…
Comment: transanno liftvcf "Error: length of chromosome [chr] is not equal to length in c
by
ezz3
• 0
Thanks. I was wondering if that is the case but was having some issues understanding the transanno code which is written in rust and I don…
Answer: Multi-ploid data in ANGSD and NGSadmix
by
andersdetermig
▴ 20
1 ) I would not expect the haploid individuals to always cluster together but the model assumptions are violated. First of all the diploid…
Comment: transanno liftvcf "Error: length of chromosome [chr] is not equal to length in c
by
Pierre Lindenbaum
161k
"Are you using correct reference?" may be your reference is not using the same chrM. see https://www.biostars.org/p/199796/#199803
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
by
shpak.max
▴ 50
Could you please elaborate on what you mean by passing -L or -V, i.e. what would the appropriate argument be for -L with UnifiedGenotyper f…
Answer: Add stats to the plot
by
Ghada
• 0
It works. I have added this code my_comparisons=list(c("HRSV", "HRSV_RBV")) plot + stat_compare_means(method = "wilcox.test",…
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
by
LChart
3.9k
I believe UnifiedGenotyper is a locus walker that sets `emitEmptySites() = False`. As such you will not see entries for positions that have…
Comment: Problem in getting geo file through GEOQUERY
by
anasjamshed
▴ 120
Basically this is my code: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") # # pkgs <- rowna…
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
by
shpak.max
▴ 50
If that were the case, I would expect there not to be any uncalled sites in the vcf, yet there are a large number of sites with "." placeho…
Comment: Problem in getting geo file through GEOQUERY
by
bk11
★ 2.5k
It just runs fine for me with just a single line of code. library(GEOquery) GSE1145 <- getGEO("GSE1145", GSEMatrix=TRUE) …
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