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757 results • Page
2 of 16
Sort: replies
Rank
Views
Votes
Replies
0
votes
9
replies
602
views
Applying the metacell2 algorithm using python
python
single-cell
scanpy
metacell2
updated 2 days ago by
Wayne
★ 2.0k • written 11 days ago by
JACKY
▴ 140
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
1.4k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq
Cellranger
STARsolo
10X
updated 27 days ago by
swbarnes2
14k • written 9 months ago by
bp22
▴ 80
0
votes
8
replies
461
views
Error in cnetplot enrichplot package
R
updated 25 days ago by
Ram
43k • written 25 days ago by
Farhad
• 0
1
vote
8
replies
550
views
Downsampling fastq file
downsample
fastq
17 days ago by
marco.barr
▴ 130
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
2
votes
8
replies
380
views
joint callset and vcf sorting, unknown TAG issue
sort
bcftools
GLNexus
merge
VCF
updated 5 days ago by
Pierre Lindenbaum
161k • written 5 days ago by
Matteo Ungaro
▴ 100
0
votes
8
replies
531
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
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
4
votes
8
replies
767
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 20 days ago by
Alex Reynolds
35k • written 21 days ago by
J
▴ 10
0
votes
8
replies
456
views
Different output for read length
samtools
BAM
8 days ago by
marco.barr
▴ 130
1
vote
8
replies
951
views
Adding CB tag to bam file
samtools
bam
updated 22 days ago by
Pierre Lindenbaum
161k • written 29 days ago by
Maria
• 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
3
votes
8
replies
688
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
8
votes
8
replies
758
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 22 days ago by
swbarnes2
14k • written 23 days ago by
Aaliya
▴ 10
1
vote
7
replies
390
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
2 days ago by
ntsopoul
▴ 60
2
votes
7
replies
956
views
Removing duplicates
duplicates
ONT
minimap2
updated 29 days ago by
noodle
▴ 580 • written 4 weeks ago by
quentinperriere
• 0
3
votes
7
replies
414
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
4
votes
7
replies
421
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
4 days ago by
Chen
• 0
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
0
votes
7
replies
442
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 4 days ago by
Mohamed Abderrahmane
▴ 20 • written 18 days ago by
matteo.levorato
• 0
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
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
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
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
1
vote
7
replies
614
views
gvcf joint calling
WES
GATK
VCF
gVCF
19 days ago by
zihanss
• 0
5
votes
7
replies
491
views
RNA seq analysis
DESeq
RNA-seq
2 days ago by
Jacek
▴ 20
1
vote
7
replies
503
views
Downsampling long-read BAM files
nanopore
BAM
QC
ONT
downsampling
14 days ago by
eebloom
▴ 80
2
votes
7
replies
5.3k
views
6 follow
Memory usage of picard Samsort
Picard
SortSam
updated 28 days ago by
ATpoint
82k • written 7.2 years ago by
boymin2020
▴ 80
0
votes
7
replies
642
views
Post-imputation plot
michigan-imputation-server
quality-control
updated 15 days ago by
LChart
3.9k • written 18 days ago by
kl
▴ 10
1
vote
7
replies
541
views
Question regarding WGCNA
WGCNA
Network-construction
8 days ago by
deepak
• 0
9
votes
7
replies
7.2k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 6 days ago by
Ruqaiya
• 0 • written 5.7 years ago by
xiaozhongzhiping
▴ 20
1
vote
7
replies
614
views
ScRNA data question
scRNA
Vlnplot
Samples
updated 18 days ago by
bk11
★ 2.5k • written 22 days ago by
starswillfade
▴ 10
6
votes
7
replies
387
views
Longest transcript variant per gene
transcript
longest
variant
orthofinder
5 days ago by
sansan_96
▴ 90
4
votes
7
replies
445
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
updated 14 hours ago by
marco.barr
▴ 130 • written 2 days ago by
diqixiaoyaoer
▴ 20
4
votes
7
replies
609
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 22 days ago by
dsull
★ 6.0k • written 23 days ago by
VITALA
• 0
0
votes
6
replies
2.1k
views
Copy number Variation analysis using conumee
R
software error
sequencing
genome
updated 8 days ago by
GenoMax
142k • written 3.2 years ago by
gs000095
▴ 10
0
votes
6
replies
421
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
genomics
plink
updated 4 days ago by
Ram
43k • written 7 days ago by
ajbarrett98
• 0
10
votes
6
replies
10k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly
rna-seq
alignment
updated 21 days ago by
Antonio R. Franco
★ 5.1k • written 6.0 years ago by
williamsbrian5064
▴ 520
5
votes
6
replies
603
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 17 days ago by
me
▴ 760 • written 18 days ago by
Mariana
▴ 40
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
3.9k
views
Taking the difference of two VCFs (or removing singletons)
genome
sequencing
singleton
SNP
filter
updated 17 days ago by
Andres
▴ 20 • written 9.7 years ago by
hermathena
▴ 40
0
votes
6
replies
224
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
5 hours ago by
hannes.bongartz
• 0
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq
RNA-Seq
exon
updated 11 days ago by
Sara
▴ 30 • written 6.7 years ago by
Lila M
★ 1.2k
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
1
vote
6
replies
2.8k
views
Segmentation fault using gemma
gemma
gwas
updated 18 days ago by
dimpleadiwal050896
• 0 • written 5.0 years ago by
ggman
▴ 90
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
7
votes
6
replies
598
views
Filtering sam or bam file with maximum matching region
crisper-edited
alignment
match
26 days ago by
analyst
▴ 50
4
votes
6
replies
1.2k
views
Soft-clipping read ends based on read group
ancient
molecule
at
bam
DNA
RG
ends
clipping
damage
updated 9 days ago by
chenl
▴ 10 • written 2.5 years ago by
Martyna
• 0
2
votes
6
replies
387
views
BWA alignment
Samtools
bam
updated 2 days ago by
a.alnawfal.1992
▴ 260 • written 5 days ago by
Vahid
• 0
757 results • Page
2 of 16
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Comment: How to handle duplicated genes in TCGA data?
by
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.
Answer: Design for complex RNA-Seq experiment using Deseq2
by
swbarnes2
14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
Comment: GG Sankey plot
by
LauferVA
4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
Answer: GG Sankey plot
by
bk11
★ 2.5k
You need to change your data table into a 'long' format. You can do something like this- GOs_childs_recursive <- GOs_childs_recursive …
Answer: Trimming tool
by
ntsopoul
▴ 60
I use Trim Galore which automatically recognizes adaptors. https://github.com/FelixKrueger/TrimGalore Here is the script I am using for…
Answer: Trimming tool
by
GenoMax
142k
There are plenty. `bbduk.sh` from BBMap suite (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ )…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
bk11
★ 2.5k
Please check out [in this link.][1] [1]: https://github.com/jokergoo/ComplexHeatmap/issues/349
Comment: Reconstruction of locus, order contigs
by
dthorbur
★ 2.0k
[Here](https://www.biostars.org/p/9544689/) is a forum post that may answer your question.
Comment: how to treat the replicates while performing WGCNA
by
andres.firrincieli
3.6k
> 1) I do not want to merge the MEs rather I asked about replicates, as > some replicates of same sample are showing different behavior for…
Comment: How to systematically check if a bam file is truncated
by
alanh
▴ 170
For more details about what `samtools quickcheck` actually checks for, add a few `-v`'s to the command line. $ samtools quickcheck -…
Comment: How to handle duplicated genes in TCGA data?
by
Zhenyu Zhang
★ 1.2k
Second what is said above, ensembl_id is the unique identifier. As a good bioinformatics habit, always use unique identifier for your anal…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
It doesn't work. The annotation labels are still in a default fontsize. I cant find a way to set the fontsize.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
Ram
43k
Yes. The solution to most things with ComplexHeatmap is to play around with parameters.
Comment: Reconstruction of locus, order contigs
by
BATMAN
• 0
I do not want to re-annotate the genome. I ask if there is a way to extract the region aligned with the mauve, in .gbk format.
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