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683 results • Page
2 of 14
Sort: replies
Rank
Views
Votes
Replies
3
votes
8
replies
1.4k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq
Cellranger
STARsolo
10X
updated 28 days ago by
swbarnes2
14k • written 9 months ago by
bp22
▴ 80
2
votes
8
replies
388
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
957
views
Adding CB tag to bam file
samtools
bam
updated 23 days ago by
Pierre Lindenbaum
161k • written 4 weeks ago by
Maria
• 0
0
votes
8
replies
462
views
Different output for read length
samtools
BAM
9 days ago by
marco.barr
▴ 130
1
vote
8
replies
557
views
Downsampling fastq file
downsample
fastq
18 days ago by
marco.barr
▴ 130
3
votes
8
replies
691
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 12 days ago by
Chris Dean
▴ 410 • written 16 days ago by
sovrappensiero
▴ 100
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 16 days ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
0
votes
8
replies
472
views
Error in cnetplot enrichplot package
R
updated 26 days ago by
Ram
43k • written 26 days ago by
Farhad
• 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
5
votes
7
replies
500
views
RNA seq analysis
DESeq
RNA-seq
3 days ago by
Jacek
▴ 20
2
votes
7
replies
1.4k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq
Salmon
Isoseq
updated 20 days ago by
Gordon Smyth
★ 7.2k • written 8 months ago by
Calum
▴ 10
4
votes
7
replies
427
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
5 days ago by
Chen
• 0
4
votes
7
replies
478
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 3 days ago by
diqixiaoyaoer
▴ 20
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
0
votes
7
replies
4.3k
views
B allele frequency (BAF)
snp
updated 22 hours ago by
aidangcruickshank
▴ 10 • written 3.7 years ago by
rthapa
▴ 90
1
vote
7
replies
510
views
Downsampling long-read BAM files
nanopore
BAM
QC
ONT
downsampling
15 days ago by
eebloom
▴ 80
4
votes
7
replies
639
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
19 days ago by
e.r.zakiev
▴ 210
1
vote
7
replies
617
views
gvcf joint calling
WES
GATK
VCF
gVCF
20 days ago by
zihanss
• 0
4
votes
7
replies
613
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
7
votes
7
replies
6.0k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq
SNP
updated 23 days ago by
rohitsatyam102
▴ 860 • written 6.2 years ago by
smallfish
▴ 10
6
votes
7
replies
394
views
Longest transcript variant per gene
transcript
longest
variant
orthofinder
6 days ago by
sansan_96
▴ 90
0
votes
7
replies
448
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
3
votes
7
replies
421
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
19 days ago by
salias
• 0
0
votes
7
replies
653
views
Post-imputation plot
michigan-imputation-server
quality-control
updated 16 days ago by
LChart
3.9k • written 19 days ago by
kl
▴ 10
1
vote
7
replies
545
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 19 days ago by
bk11
★ 2.5k • written 23 days ago by
starswillfade
▴ 10
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 3 days ago by
Ram
43k • written 3.9 years ago by
millere
• 0
0
votes
6
replies
499
views
Use of Kraken output for functional analysis
metagenomics
kraken
shotgun
updated 24 days ago by
gv
• 0 • written 6 weeks ago by
Srinka
▴ 20
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
7
votes
6
replies
603
views
Filtering sam or bam file with maximum matching region
crisper-edited
alignment
match
27 days ago by
analyst
▴ 50
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
2
votes
6
replies
3.8k
views
Treatment VS Control in Single Cell RNAseq analysis
Single Cell
RNAseq
DE Analysis
Treatment
Control
updated 23 days ago by
ATpoint
82k • written 3.9 years ago by
grayapply2009
▴ 280
3
votes
6
replies
760
views
Ciriquant not configuring hisat2 indexed files
ciriquant
26 days ago by
Atul K.
• 0
0
votes
6
replies
427
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
genomics
plink
updated 5 days ago by
Ram
43k • written 8 days ago by
ajbarrett98
• 0
0
votes
6
replies
490
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 15 days ago by
swbarnes2
14k • written 15 days ago by
Erina
• 0
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 10 days ago by
chenl
▴ 10 • written 2.5 years ago by
Martyna
• 0
4
votes
6
replies
809
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
0
votes
6
replies
454
views
How to slice a gvcf file with tabix?
Tabix
bed
gvcf
25 days ago by
Sd
• 0
5
votes
6
replies
607
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 18 days ago by
me
▴ 760 • written 19 days ago by
Mariana
▴ 40
1
vote
6
replies
732
views
anRichment is missing
WGCNA
anRichment
updated 12 days ago by
GenoMax
142k • written 6 months ago by
michael.flower.14
▴ 180
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
3
votes
6
replies
2.0k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 22 days ago by
Ram
43k • written 2.4 years ago by
SYOSY
▴ 10
2
votes
6
replies
397
views
BWA alignment
Samtools
bam
updated 3 days ago by
a.alnawfal.1992
▴ 260 • written 6 days ago by
Vahid
• 0
6
votes
6
replies
1.8k
views
agilent human all exon sureselct v7 bed file
exon
human
bed
v7
agilent
all
sureselect
updated 13 days ago by
MiladAD
▴ 10 • written 2.0 years ago by
soheil
• 0
1
vote
6
replies
412
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 15 days ago by
GenoMax
142k • written 4 weeks ago by
eebloom
▴ 80
3
votes
6
replies
505
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 6 days ago by
Pine
▴ 20 • written 13 days ago by
snajafy
• 0
0
votes
6
replies
294
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
1 day ago by
hannes.bongartz
• 0
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
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
0
votes
5
replies
442
views
6 follow
What purposes can TPM values be used for?
RNA-seq
TPM
Normalization
DESeq2
updated 15 days ago by
b.contreras.moreira
▴ 200 • written 16 days ago by
JH
• 0
683 results • Page
2 of 14
Recent Votes
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Error in CIBERSORTx ($ operator is invalid for atomic vectors)
Answer: RNAseq coverage vs depth for transcript isoform expression?
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Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Answer: RNAseq coverage vs depth for transcript isoform expression?
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Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors)
by
nguyenn6
• 0
did you ever figure it out? i'm having the same issue.
Comment: Traveler with Infernal mapping failed
by
anton.i.petrov
• 0
Hi Larissa! I am the lead developer of R2DT and I've just noticed this question. Could you please email help@r2dt.bio with your input seque…
Comment: constructing pangenome through psvcp
by
analyst
▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
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142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
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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.
Comment: Help with Biopython for Beginner
by
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21k
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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by
Gordon Smyth
★ 7.2k
See the exploration of isoform estimation precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167.…
Comment: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
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…
Comment: how to treat the replicates while performing WGCNA
by
mavy
▴ 10
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
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
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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35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF)
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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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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…
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