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679 results • Page
2 of 14
Sort: replies
Rank
Views
Votes
Replies
0
votes
8
replies
518
views
Different output for read length
samtools
BAM
16 days ago by
marco.barr
▴ 130
1
vote
8
replies
505
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
updated 7 days ago by
Alex Reynolds
35k • written 12 days ago by
ntsopoul
▴ 60
2
votes
8
replies
430
views
joint callset and vcf sorting, unknown TAG issue
sort
bcftools
GLNexus
merge
VCF
updated 13 days ago by
Pierre Lindenbaum
162k • written 13 days ago by
Matteo Ungaro
▴ 100
0
votes
8
replies
557
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
genomics
plink
updated 6 days ago by
Pierre Lindenbaum
162k • written 15 days ago by
ajbarrett98
• 0
3
votes
8
replies
875
views
Random Access remote BAM files
htslib
BAM
updated 3 days ago by
a.penatauber
• 0 • written 3 months ago by
Lucas R.F.
▴ 20
3
votes
8
replies
756
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 19 days ago by
Chris Dean
▴ 410 • written 23 days ago by
sovrappensiero
▴ 100
3
votes
8
replies
657
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
19 days ago by
Qroid
▴ 40
1
vote
8
replies
599
views
Downsampling fastq file
downsample
fastq
25 days ago by
marco.barr
▴ 130
0
votes
8
replies
567
views
What does it mean single base resolution in sequencing?
SNP
sequencing
updated 25 days ago by
LauferVA
4.2k • written 27 days ago by
jinyu
▴ 10
5
votes
7
replies
556
views
RNA seq analysis
DESeq
RNA-seq
10 days ago by
Jacek
▴ 20
4
votes
7
replies
654
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
26 days ago by
e.r.zakiev
▴ 210
1
vote
7
replies
642
views
ScRNA data question
scRNA
Vlnplot
Samples
updated 26 days ago by
bk11
★ 2.5k • written 4 weeks ago by
starswillfade
▴ 10
2
votes
7
replies
1.4k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq
Salmon
Isoseq
updated 27 days ago by
Gordon Smyth
★ 7.2k • written 9 months ago by
Calum
▴ 10
2
votes
7
replies
607
views
KEGG analysis in R
KEGG
clusterProfiler
Zea-mays
updated 3 days ago by
letizia.ottaviani
• 0 • written 6 weeks ago by
sansan_96
▴ 90
0
votes
7
replies
4.3k
views
B allele frequency (BAF)
snp
updated 7 days ago by
aidangcruickshank
▴ 10 • written 3.7 years ago by
rthapa
▴ 90
4
votes
7
replies
457
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
12 days ago by
Chen
• 0
1
vote
7
replies
536
views
Downsampling long-read BAM files
nanopore
BAM
QC
ONT
downsampling
22 days ago by
eebloom
▴ 80
0
votes
7
replies
690
views
Post-imputation plot
michigan-imputation-server
quality-control
updated 23 days ago by
LChart
3.9k • written 26 days ago by
kl
▴ 10
1
vote
7
replies
594
views
Question regarding WGCNA
WGCNA
Network-construction
16 days ago by
deepak
• 0
9
votes
7
replies
7.2k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 14 days ago by
Ruqaiya
• 0 • written 5.8 years ago by
xiaozhongzhiping
▴ 20
3
votes
7
replies
4.0k
views
Difference in Bismark output methylation call files and coverage files
RRBS
Bismark
DNA-methylation
updated 2 days ago by
Papyrus
★ 2.9k • written 3.9 years ago by
linelr
▴ 40
6
votes
7
replies
438
views
Longest transcript variant per gene
transcript
longest
variant
orthofinder
13 days ago by
sansan_96
▴ 90
0
votes
7
replies
490
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 12 days ago by
Mohamed Abderrahmane
▴ 20 • written 26 days ago by
matteo.levorato
• 0
3
votes
7
replies
444
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
26 days ago by
Sergio A.S.
• 0
1
vote
7
replies
635
views
gvcf joint calling
WES
GATK
VCF
gVCF
27 days ago by
zihanss
• 0
1
vote
6
replies
782
views
anRichment is missing
WGCNA
anRichment
updated 19 days ago by
GenoMax
142k • written 6 months ago by
michael.flower.14
▴ 180
3
votes
6
replies
2.1k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 29 days ago by
Ram
44k • written 2.4 years ago by
SYOSY
▴ 10
6
votes
6
replies
1.9k
views
agilent human all exon sureselct v7 bed file
exon
human
bed
v7
agilent
all
sureselect
updated 20 days ago by
MiladAD
▴ 10 • written 2.0 years ago by
soheil
• 0
0
votes
6
replies
2.2k
views
Copy number Variation analysis using conumee
R
software error
sequencing
genome
updated 16 days ago by
GenoMax
142k • written 3.2 years ago by
gs000095
▴ 10
3
votes
6
replies
346
views
Problem in getting geo file through GEOQUERY
geoquery
Geo
updated 3 days ago by
Ram
44k • written 4 days ago by
anasjamshed
▴ 120
1
vote
6
replies
375
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
4 days ago by
Umer
▴ 50
1
vote
6
replies
334
views
samtools write-index
samtools
updated 2 days ago by
aw7
▴ 310 • written 3 days ago by
LucisTheFather
• 0
1
vote
6
replies
1.5k
views
CellRanger output more cells than specified using --force-cells? Why?
scRNA-seq
cellranger
updated 6 days ago by
scideas
▴ 30 • written 8 months ago by
rohitsatyam102
▴ 870
2
votes
6
replies
310
views
How to get the ratio of allele counts from GATK derived VCF file?
Freebayes
GATK
SNP
VCF
2 days ago by
anikcropscience
▴ 230
1
vote
6
replies
2.8k
views
Segmentation fault using gemma
gemma
gwas
updated 26 days ago by
dimpleadiwal050896
• 0 • written 5.0 years ago by
ggman
▴ 90
1
vote
6
replies
441
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 22 days ago by
GenoMax
142k • written 5 weeks ago by
eebloom
▴ 80
0
votes
6
replies
278
views
from CRAM to fastq
FASTQ
WGS
CRAM
updated 3 days ago by
ATpoint
82k • written 3 days ago by
machaalani29
• 0
4
votes
6
replies
386
views
Mouse or Rat Gene Expression Data Similar to GTEx
whole-body
expression
atlas
2 days ago by
Shicheng Guo
★ 9.4k
4
votes
6
replies
3.9k
views
Taking the difference of two VCFs (or removing singletons)
genome
sequencing
singleton
SNP
filter
updated 25 days ago by
Andres
▴ 20 • written 9.7 years ago by
hermathena
▴ 40
5
votes
6
replies
649
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 25 days ago by
me
▴ 760 • written 26 days ago by
Mariana
▴ 40
10
votes
6
replies
10k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly
rna-seq
alignment
updated 29 days ago by
Antonio R. Franco
★ 5.1k • written 6.1 years ago by
williamsbrian5064
▴ 520
4
votes
6
replies
840
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 28 days ago by
dsull
★ 6.1k • written 4 weeks ago by
qudrat.nii
▴ 10
2
votes
6
replies
307
views
Error with BiocParallel. No barcodes files found
Barcodes
scRNA-seq
SingleCellExperiment
1 day ago by
bio_info
▴ 10
2
votes
6
replies
2.0k
views
How can you *consistently* download BioProject IDs from NCBI's BioSample database using Entrez Direct?
XML
ncbi
entrez-direct
updated 10 days ago by
Ram
44k • written 3.9 years ago by
millere
• 0
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq
RNA-Seq
exon
updated 19 days ago by
Sara
▴ 30 • written 6.7 years ago by
Lila M
★ 1.3k
3
votes
6
replies
547
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 13 days ago by
Pine
▴ 20 • written 20 days ago by
snajafy
• 0
2
votes
6
replies
433
views
BWA alignment
Samtools
bam
updated 10 days ago by
a.alnawfal.1992
▴ 260 • written 13 days ago by
Vahid
• 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 17 days ago by
chenl
▴ 10 • written 2.6 years ago by
Martyna
• 0
0
votes
6
replies
520
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 22 days ago by
swbarnes2
14k • written 22 days ago by
Erina
• 0
0
votes
5
replies
203
views
Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files
Bowtie
1 day ago by
Deepthi
• 0
679 results • Page
2 of 14
Recent Votes
Low DESeq2 Sensivity on scRNA Pseudobulk Samples
DESEQ2: How can I convert ensembl gene id's to HGNC gene names.
Problem with Ensembl version identifiers after running DESeq2
Issues with adding gene name and entrez ID to DESeq2 result having Ensembl ID.
A: Looking for differential gene expression between treatment, within a specific cl
How to compare cell-type ratios in sc-RNA seq data?
How to calculate cell type frequency between two groups in single cell data
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Recent Replies
Comment: Merging multiple samples in Seurat
by
Picasa
▴ 640
did you split by sample or donor ?
Comment: Harmony integration group.by.var parameter
by
Picasa
▴ 640
For downstream analysis, after integration, my plan is to annotate each cluster/cell type and then perform a DGE analysis of KO versus WT f…
Comment: How to calculate cell type frequency between two groups in single cell data
by
Bastien Hervé
5.3k
That is correct
Answer: Setting a threshold on gene expression for subsetting (scRNA-seq)
by
ATpoint
82k
That depends on the data and the marker. Generally I would plot violins per cluster for the marker(s) and see whether one robustly overexpr…
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by
peanut
• 0
thank you so much ,i get it
Comment: Number of non-ATCG nucleotides replaced by Salmon
by
Tonya S.
▴ 10
Oops, yes, that must be where they are coming from. For some reason, I was thinking the genome was just soft-masked. How embarrassing! Than…
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6.6k
If there are no other signs that anything is awry, I probably wouldn't worry about this. Is it possible that these non-canonical nucleotid…
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I examined nine 10B runs and five 25B runs (we just started getting 25B flowcells a few months ago). I did not pay close attention but it …
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> I don't know how widespread these issues are outside of JGI. Very few small/medium sequencing centers likely have NovaSeq X. This is the…
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Supporting figures, taken from some slides I prepared for internal use. HDist 0, 1, and 2 correspond to 0, 1, and 2 mismatches allowed in …
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This works. Thank you so so much!
Comment: Harmony integration group.by.var parameter
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jared.andrews07
★ 17k
>I am not sure, but using "Sample_ID" might remove the differences between the conditions right ? More than likely, it'd at least impact t…
Comment: Harmony integration group.by.var parameter
by
Picasa
▴ 640
Thanks jared.andrews07 for your answer. So, you are suggesting to use only "Donor" in the integration? ```r RunHarmony(seu_obj, group.by.…
Comment: Single cell analysis: Unable to subset cells in seurat object using desired nFea
by
sc_analysis
• 0
I am not sure what should be the cut off. Looking at the vlnplot before subsetting i thought most of the cells are falling under 7500 nfeat…
Comment: How to calculate cell type frequency between two groups in single cell data
by
Sara
▴ 30
Thank you for your comment and sorry if this question might be so basic. How can I normalize the number of cells? If I am not wrong the i…
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