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1,000 results • Page
2 of 20
Sort: Views
Rank
Views
Votes
Replies
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
★ 1.2k
2
votes
4
replies
3.8k
views
Converting different annotation file formats (GTF/GFF/BED) to each other
rna-seq
next-gen
updated 7 months ago by
alejandrogzi
▴ 120 • written 6.7 years ago by
Javad
▴ 150
10
votes
7
replies
3.7k
views
What is Pathway Analysis?
database
analysis
ontology
pathway
updated 11 months ago by
Ram
44k • written 8.1 years ago by
Pranavathiyani G
▴ 330
5
votes
8
replies
3.7k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression
RNA-seq
gene-ontology
updated 6 weeks ago by
Ram
44k • written 6.6 years ago by
firestar
★ 1.6k
0
votes
4
replies
3.6k
views
SNPEff database building error
SNP
updated 11 days ago by
Fungal genetics
• 0 • written 7.2 years ago by
ntyagi654
• 0
1
vote
2
replies
3.6k
views
rna-seq analysis with Salmon - how to Import and summarize using tximport
RNA-Seq
salmon
tximport
updated 7 months ago by
camillab.
▴ 160 • written 4.7 years ago by
woojoy14
▴ 10
4
votes
12
replies
3.5k
views
How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
variant-calling
samtools
VCF
BCF
updated 8 weeks ago by
Ram
44k • written 5.6 years ago by
c.clarido
▴ 110
0
votes
2
replies
3.5k
views
dN/dS ratio from .vcf file
synonmous
non-synomous
mutation
updated 7 months ago by
rohitsatyam102
▴ 870 • written 5.5 years ago by
shubhra.bhattacharya
▴ 140
3
votes
4
replies
3.5k
views
Switch ref/alt alleles vcf file
SNP
vcf
sequencing
updated 4 months ago by
jvt
• 0 • written 4.5 years ago by
mdstep
▴ 20
4
votes
8
replies
3.5k
views
How to reduce the number of SNPs for the Lositan software
Lositan
SNP
updated 11 months ago by
Ram
44k • written 9.6 years ago by
zhaojianli198322
• 0
1
vote
8
replies
3.5k
views
Best way to address different batches of RNA-seq
sequence
RNA-Seq
RPKM
Fold-Change
batch-effect
updated 5 weeks ago by
Ram
44k • written 7.1 years ago by
tud55122
▴ 20
2
votes
10
replies
3.5k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 5 weeks ago by
Ram
44k • written 7.5 years ago by
linda
• 0
3
votes
4
replies
3.5k
views
any recommended tools for batch effect and normalization not written in R?
R
RNA-Seq
combat
python
batch-effect
updated 5 weeks ago by
Ram
44k • written 7.2 years ago by
dyollluap
▴ 310
0
votes
4
replies
3.4k
views
Polyploidy found, and not supported by vcftools
SNP
updated 11 months ago by
Ram
44k • written 5.3 years ago by
sambioinfo2018
▴ 20
1
vote
1
reply
3.4k
views
Problem with PGDSpider v 2.1.0.2
alignment
updated 11 months ago by
sackettl
▴ 20 • written 7.9 years ago by
maria.segovia.ramirez
▴ 10
1
vote
2
replies
3.4k
views
How to convert FASTA to NEXUS in Python
fasta
biopython
nexus
updated 10 months ago by
Ram
44k • written 3.8 years ago by
adrian18_07
▴ 10
20
votes
17
replies
3.4k
views
How to add "transcript" feature to a gtf file?
gtf
updated 10 months ago by
1769mkc
★ 1.2k • written 3.3 years ago by
pomodoro_sinensis
▴ 110
2
votes
12
replies
3.4k
views
WCGNA installation help
R
WGCNA
updated 3 months ago by
Ram
44k • written 5.0 years ago by
prekrish
• 0
1
vote
9
replies
3.4k
views
build databses for genome using snpEff
annotation
SNP
snpEff
updated 9 months ago by
nehakhilwani18
• 0 • written 5.8 years ago by
StudentBio
• 0
2
votes
5
replies
3.3k
views
How to output colored alignment from clustal omega stand alone tool?
Clustal Omega
Colored alignment
updated 9 months ago by
Joe
21k • written 4.8 years ago by
MB
▴ 50
1
vote
6
replies
3.3k
views
Filter VCF file
snp
next-gen
updated 11 months ago by
Ram
44k • written 7.9 years ago by
sukesh1411
▴ 30
3
votes
6
replies
3.3k
views
samtools sort not working when using multiple threads
samtools
bam
updated 11 months ago by
Ram
44k • written 2.3 years ago by
bio_elle
▴ 10
0
votes
1
reply
3.3k
views
Cutadapt 1.9.1 error
cutadapt
next-gen
updated 11 months ago by
Ram
44k • written 8.3 years ago by
vishweshwaransridhar
▴ 10
3
votes
7
replies
3.3k
views
vcf filter for FORMAT argument (DP/GQ/GQX > 30) multiple (380) vcf file
vcffilter
vcftools
sequencing
updated 11 months ago by
Ram
44k • written 4.2 years ago by
IndyDNA
▴ 10
2
votes
10
replies
3.2k
views
6 follow
Split plink files by a number of SNPs
GWAS
SNP
plink
updated 7 months ago by
Raygozak
★ 1.4k • written 5.9 years ago by
kakukeshi
▴ 80
3
votes
5
replies
3.2k
views
GO annotation for rice in an R package
annotation
R
updated 4 months ago by
prity6459
• 0 • written 7.5 years ago by
djyjin
▴ 10
5
votes
7
replies
3.2k
views
8 follow
bwa mem -T (alignment score) not doing anything
SNP
genome
sequence
updated 7 months ago by
Istvan Albert
100k • written 6.0 years ago by
chris.bird
▴ 10
0
votes
1
reply
3.2k
views
How to convert g.vcf to .vcf file
vcf
sequence
genome
alignment
updated 11 months ago by
Ram
44k • written 5.1 years ago by
Sakhaa
• 0
2
votes
6
replies
3.2k
views
hisat2 :Killed (ERR): hisat2-align exited with value 137
RNA-seq
alignment
hisat2
updated 9 months ago by
Ram
44k • written 2.4 years ago by
iamsmor
• 0
0
votes
1
reply
3.2k
views
PSMC plot (Effective population size)
next-gen
updated 8 months ago by
1601693223
• 0 • written 8.5 years ago by
vicky
▴ 30
1
vote
7
replies
3.1k
views
RGT TypeError: unsupported operand type(s) for +: 'NoneType' and 'int'
RGT
TF-footprinting
ATAC-seq
updated 11 months ago by
Ram
44k • written 5.5 years ago by
grant.hovhannisyan
★ 2.6k
1
vote
10
replies
3.1k
views
How to specify/calculate subject coverage of the alignment (alignment of query[protein sequence] and subject[Nucleotide sequence]) in tBLASTn?
alignment
BLAST
tBLASTn
updated 12 months ago by
Ram
44k • written 5.2 years ago by
Kumar
▴ 120
3
votes
12
replies
3.1k
views
What is NCBI Gene ID, where to find it and how to convert to entrez ID?
RNA-Seq
updated 11 months ago by
Pegasus
▴ 100 • written 4.6 years ago by
mnazir
▴ 10
3
votes
6
replies
3.1k
views
Which of the 4 SureSelect Agilent BED files to use with GATK haplotype caller?
gatk
variant calling
sureselect
updated 10 months ago by
LeandroF.
• 0 • written 4.3 years ago by
curious
▴ 750
1
vote
5
replies
3.1k
views
Problem in running NOISeq-sim
NOISeq
RNA-Seq
updated 11 months ago by
Ram
44k • written 5.8 years ago by
jaspreetk.dhanjal
▴ 20
0
votes
3
replies
3.1k
views
Rna-seq for differential expression analysis
differential-expression
transcriptome
updated 5 weeks ago by
Ram
44k • written 9.0 years ago by
siddharth.patel.153
• 0
0
votes
2
replies
3.1k
views
How to convert gbk file to roary tool acceptable gff3 format?
linux
bash
python
perl
updated 11 months ago by
Ram
44k • written 3.7 years ago by
Kumar
▴ 120
2
votes
3
replies
3.0k
views
RNA-seq batch effect correction
RNA-Seq
batch-effect
sequencing
updated 5 weeks ago by
Ram
44k • written 7.0 years ago by
endikavarela
• 0
6
votes
9
replies
3.0k
views
How to analyze the scRNA seq Fastq files from NCBI
SRAtool
Cellranger
NCBI
updated 11 months ago by
Ram
44k • written 2.4 years ago by
aimanbarki
▴ 20
0
votes
1
reply
3.0k
views
RNA-seq compare FPKM's or fold change of different organisms
gene-expression
FPKM
RNA-seq
fold-change
updated 8 months ago by
Ram
44k • written 6.8 years ago by
jehu
▴ 30
0
votes
7
replies
2.9k
views
qPCR: Huge variation in fold change of genes between biological replicates
qpcr
fold-change
updated 8 months ago by
Ram
44k • written 5.9 years ago by
AP
▴ 80
2
votes
3
replies
2.9k
views
Merge really large amount of Seurat objects
Seurat
11 months ago by
Andy
▴ 120
0
votes
0
replies
2.9k
views
TCGA RNAseqVer2 batch effects
TCGA
RNA-Seq
batch-effect
updated 5 weeks ago by
Ram
44k • written 8.6 years ago by
annadv
• 0
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
3
votes
3
replies
2.8k
views
WGCNA Labeled Heatmap
heatmap
wgcna
updated 8 months ago by
Ram
44k • written 2.7 years ago by
Anand
▴ 40
0
votes
3
replies
2.8k
views
Generate GTF/GFF file (coordinates) from a FASTA annotated file.
Assembly
genome
updated 11 months ago by
Ram
44k • written 4.7 years ago by
marquezg48
• 0
0
votes
2
replies
2.8k
views
RNA-seq unbalanced batch effect correction
limma
RNA-Seq
edgeR
batch-effect
updated 5 weeks ago by
Ram
44k • written 7.1 years ago by
endikavarela
• 0
1
vote
4
replies
2.8k
views
removing confounding batch effect with RUVseq
RUVseq
RNA-Seq
batch-effect
DESeq2
updated 5 weeks ago by
Ram
44k • written 5.2 years ago by
grant.hovhannisyan
★ 2.6k
0
votes
3
replies
2.8k
views
Circos plot for ecoli genome
rna-seq
circos
updated 9 months ago by
Ram
44k • written 7.4 years ago by
raya.girish
▴ 30
1
vote
1
reply
2.8k
views
Comparing time series expression data
time-series
gene-expression
updated 12 months ago by
Ram
44k • written 6.8 years ago by
The
▴ 180
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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
DESeq2 single cell pseudobulk
Comment: Number of non-ATCG nucleotides replaced by Salmon
Answer: Number of non-ATCG nucleotides replaced by Salmon
Answer: Error when i use EVidenceModeler to do the genome annotation
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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…
Comment: Error when i use EVidenceModeler to do the genome annotation
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…
Answer: Number of non-ATCG nucleotides replaced by Salmon
by
Rob
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…
Comment: Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvage
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Brian Bushnell
20k
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 …
Comment: Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvage
by
GenoMax
142k
> 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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by
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20k
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 …
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
This works. Thank you so so much!
Comment: Harmony integration group.by.var parameter
by
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…
Comment: Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files
by
Deepthi
• 0
I unzipped the fastq files to check whether reads are trimmed adapter or not. I have checked the quality control using fastqc they are go…
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