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747 results • Page
2 of 15
Sort: replies
Rank
Views
Votes
Replies
0
votes
8
replies
465
views
Error in cnetplot enrichplot package
R
updated 25 days ago by
Ram
43k • written 25 days ago by
Farhad
• 0
2
votes
8
replies
385
views
joint callset and vcf sorting, unknown TAG issue
sort
bcftools
GLNexus
merge
VCF
updated 6 days ago by
Pierre Lindenbaum
161k • written 6 days ago by
Matteo Ungaro
▴ 100
1
vote
8
replies
555
views
Downsampling fastq file
downsample
fastq
17 days ago by
marco.barr
▴ 130
8
votes
8
replies
763
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 23 days ago by
swbarnes2
14k • written 24 days ago by
Aaliya
▴ 10
1
vote
8
replies
430
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
updated 9 hours ago by
Alex Reynolds
35k • written 4 days ago by
ntsopoul
▴ 60
3
votes
8
replies
5.0k
views
An idea to identify batch effects
microarray
batch-effect
updated 29 days ago by
Ram
43k • written 9.7 years ago by
mjarosz
• 0
3
votes
8
replies
4.2k
views
Using FPKM and TPM values for batch correction for Single Cell RNA-Seq
fpkm
scRNA-seq
RNA-Seq
tpm
batch-effect
updated 29 days ago by
Ram
43k • written 4.6 years ago by
hkarakurt
▴ 180
1
vote
8
replies
952
views
Adding CB tag to bam file
samtools
bam
updated 23 days ago by
Pierre Lindenbaum
161k • written 29 days ago by
Maria
• 0
0
votes
8
replies
462
views
Different output for read length
samtools
BAM
8 days ago by
marco.barr
▴ 130
4
votes
8
replies
772
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 21 days ago by
Alex Reynolds
35k • written 22 days ago by
J
▴ 10
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 15 days ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
0
votes
8
replies
534
views
What does it mean single base resolution in sequencing?
SNP
sequencing
updated 17 days ago by
LauferVA
4.2k • written 19 days ago by
jinyu
▴ 10
3
votes
8
replies
602
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
11 days ago by
Qroid
▴ 40
3
votes
8
replies
690
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 11 days ago by
Chris Dean
▴ 410 • written 15 days ago by
sovrappensiero
▴ 100
4
votes
7
replies
463
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
updated 1 day ago by
marco.barr
▴ 130 • written 2 days ago by
diqixiaoyaoer
▴ 20
3
votes
7
replies
419
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
18 days ago by
salias
• 0
2
votes
7
replies
961
views
Removing duplicates
duplicates
ONT
minimap2
updated 29 days ago by
noodle
▴ 580 • written 4 weeks ago by
quentinperriere
• 0
0
votes
7
replies
446
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 5 days ago by
Mohamed Abderrahmane
▴ 20 • written 19 days ago by
matteo.levorato
• 0
1
vote
7
replies
508
views
Downsampling long-read BAM files
nanopore
BAM
QC
ONT
downsampling
15 days ago by
eebloom
▴ 80
7
votes
7
replies
6.0k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq
SNP
updated 22 days ago by
rohitsatyam102
▴ 860 • written 6.2 years ago by
smallfish
▴ 10
0
votes
7
replies
649
views
Post-imputation plot
michigan-imputation-server
quality-control
updated 15 days ago by
LChart
3.9k • written 18 days ago by
kl
▴ 10
4
votes
7
replies
611
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 23 days ago by
dsull
★ 6.0k • written 24 days ago by
VITALA
• 0
2
votes
7
replies
5.3k
views
6 follow
Memory usage of picard Samsort
Picard
SortSam
updated 29 days ago by
ATpoint
82k • written 7.2 years ago by
boymin2020
▴ 80
1
vote
7
replies
542
views
Question regarding WGCNA
WGCNA
Network-construction
9 days ago by
deepak
• 0
1
vote
7
replies
618
views
ScRNA data question
scRNA
Vlnplot
Samples
updated 18 days ago by
bk11
★ 2.5k • written 23 days ago by
starswillfade
▴ 10
6
votes
7
replies
393
views
Longest transcript variant per gene
transcript
longest
variant
orthofinder
5 days ago by
sansan_96
▴ 90
2
votes
7
replies
1.4k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq
Salmon
Isoseq
updated 19 days ago by
Gordon Smyth
★ 7.2k • written 8 months ago by
Calum
▴ 10
6
votes
7
replies
1.6k
views
How to assess RNA-Seq batch correction success?
Combat
RNA-Seq
Limma
DESeq2
batch-effect
updated 29 days ago by
Ram
43k • written 5.0 years ago by
borkk
▴ 140
4
votes
7
replies
424
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
4 days ago by
Chen
• 0
4
votes
7
replies
635
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
18 days ago by
e.r.zakiev
▴ 210
9
votes
7
replies
7.2k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 7 days ago by
Ruqaiya
• 0 • written 5.7 years ago by
xiaozhongzhiping
▴ 20
1
vote
7
replies
616
views
gvcf joint calling
WES
GATK
VCF
gVCF
20 days ago by
zihanss
• 0
0
votes
7
replies
1.9k
views
Batch effect correction in RNASeq data and plot Dendrograms cluster
clustering
dendrogram
RNA-Seq
batch-effect
updated 29 days ago by
Ram
43k • written 4.1 years ago by
Ankit
▴ 500
0
votes
7
replies
4.3k
views
B allele frequency (BAF)
snp
updated 9 hours ago by
aidangcruickshank
▴ 10 • written 3.7 years ago by
rthapa
▴ 90
5
votes
7
replies
498
views
RNA seq analysis
DESeq
RNA-seq
3 days ago by
Jacek
▴ 20
3
votes
6
replies
493
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 5 days ago by
Pine
▴ 20 • written 12 days ago by
snajafy
• 0
0
votes
6
replies
268
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
16 hours ago by
hannes.bongartz
• 0
3
votes
6
replies
2.0k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 21 days ago by
Ram
43k • written 2.4 years ago by
SYOSY
▴ 10
10
votes
6
replies
14k
views
7 follow
How To Identify The 16S Rrna Gene Sequence In A Genome
updated 29 days ago by
colindaven
6.4k • written 10.9 years ago by
Ontheway
▴ 10
0
votes
6
replies
450
views
How to slice a gvcf file with tabix?
Tabix
bed
gvcf
24 days ago by
Sd
• 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 2 days ago by
Ram
43k • written 3.9 years ago by
millere
• 0
2
votes
6
replies
5.3k
views
How to avoid over-correction by using harmony or CCA to batch correction in scRNA-seq?
scRNA-seq
R
seurat
harmony
batch-effect
updated 29 days ago by
Ram
43k • written 3.8 years ago by
Lukadon77
• 0
4
votes
6
replies
808
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 21 days ago by
dsull
★ 6.0k • written 25 days ago by
qudrat.nii
▴ 10
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq
RNA-Seq
exon
updated 12 days ago by
Sara
▴ 30 • written 6.7 years ago by
Lila M
★ 1.2k
0
votes
6
replies
490
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 14 days ago by
swbarnes2
14k • written 15 days ago by
Erina
• 0
7
votes
6
replies
600
views
Filtering sam or bam file with maximum matching region
crisper-edited
alignment
match
26 days ago by
analyst
▴ 50
1
vote
6
replies
2.8k
views
Segmentation fault using gemma
gemma
gwas
updated 19 days ago by
dimpleadiwal050896
• 0 • written 5.0 years ago by
ggman
▴ 90
4
votes
6
replies
3.9k
views
Taking the difference of two VCFs (or removing singletons)
genome
sequencing
singleton
SNP
filter
updated 18 days ago by
Andres
▴ 20 • written 9.7 years ago by
hermathena
▴ 40
0
votes
6
replies
2.1k
views
Copy number Variation analysis using conumee
R
software error
sequencing
genome
updated 9 days ago by
GenoMax
142k • written 3.2 years ago by
gs000095
▴ 10
10
votes
6
replies
10k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly
rna-seq
alignment
updated 22 days ago by
Antonio R. Franco
★ 5.1k • written 6.0 years ago by
williamsbrian5064
▴ 520
747 results • Page
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Comment: calculating genomic coverage/ base overlap in R
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★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks
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82k
What is your question? It's unclear.
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One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
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★ 7.2k
See the exploration of isoform precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167. Table 1 o…
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Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
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Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
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i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
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Yes, `bedmap` will perform operations on one or two BED files.
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▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data?
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Ngrin
• 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
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Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
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You need to change your data table into a 'long' format. You can do something like this- GOs_childs_recursive <- GOs_childs_recursive …
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