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117,132 results • Page
2 of 2343
Sort: Rank
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Views
Votes
Replies
0
votes
2
replies
233
views
How do we do quantification using stringtie merge option for all the merged samples generated.
stringtie
quantification
updated 2 days ago by
i.sudbery
19k • written 3 days ago by
Varsha
• 0
3
votes
2
replies
173
views
How to interpret this plotMDS of three disease clusters?
microarray
plotMDS
DEGs
updated 2 days ago by
ATpoint
82k • written 2 days ago by
egascon
• 0
0
votes
0
replies
87
views
GWAS or QTL mapping in RIL population
GWAS
RIL
2 days ago by
韩雨
• 0
0
votes
0
replies
90
views
VEP annotation tool: "." isn't numeric in addition (+)
VEP
VCF
updated 1 day ago by
Ram
44k • written 2 days ago by
emmanouil.a
▴ 120
11
votes
13
replies
6.7k
views
7 follow
log2 fold change in RNA-seq analysis
fold
log2
change
updated 1 day ago by
May Ling
• 0 • written 2.4 years ago by
wmsalsah
▴ 10
0
votes
1
reply
264
views
GWAS Phenotypes
GWAS
updated 2 days ago by
韩雨
• 0 • written 5 weeks ago by
solomoncharles77
▴ 90
5
votes
4
replies
5.2k
views
6 follow
Classic threshold for log2 fold change in RNA-seq experiment
RNA-Seq
updated 2 days ago by
May Ling
• 0 • written 3.9 years ago by
Mozart
▴ 330
1
vote
1
reply
126
views
Cellranger-multi : Demultiplexing and Analyzing 5’ Immune Profiling Libraries Pooled with Hashtags
5InmuneProfiling
nf-core
scRNAseq
cellranger-multi
Nextflow
updated 2 days ago by
GenoMax
142k • written 2 days ago by
azeu
▴ 10
0
votes
0
replies
62
views
Assigning Micro-C read pairs to nucleosomes called from MNase-seq data?
Hi-C
MNase-Seq
2 days ago by
Linus
• 0
7
votes
3
replies
13k
views
Z score in RNAseq
RNA-Seq
Zscore
updated 2 days ago by
Akash D
▴ 60 • written 6.5 years ago by
rob.costa1234
▴ 310
0
votes
1
reply
142
views
Free AI for R programming
R
updated 1 day ago by
Ram
44k • written 2 days ago by
mohamadzare6022
▴ 10
7
votes
13
replies
823
views
7 follow
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 1 day ago by
i.sudbery
19k • written 4 weeks ago by
Estevão
▴ 10
0
votes
0
replies
95
views
Extracting haplotype-specific annotations from splicing graph
vg
2 days ago by
Juhyun
• 0
0
votes
0
replies
90
views
miloR - object 'as.SimpleList' of mode 'function' was not found when running calcNhoodDistance
scRNA-seq
seurat
miloR
2 days ago by
shuaizh117
▴ 10
0
votes
0
replies
90
views
Phyloseq returning black bars for plot_bar
phyloseq
bioconductor
R
2 days ago by
Jacob
• 0
3
votes
8
replies
874
views
Random Access remote BAM files
htslib
BAM
updated 2 days ago by
a.penatauber
• 0 • written 3 months ago by
Lucas R.F.
▴ 20
0
votes
0
replies
96
views
Cancer vs Normal Cell Classification Based on SNVs
cancer
2 days ago by
dglad
• 0
0
votes
4
replies
217
views
merge overlaps and remove non overlap genomic windows
BED
intersection
overlap
2 days ago by
reza
▴ 300
0
votes
1
reply
129
views
Flag multiple filtering steps on VCF files using VEP
VEP
VCF
updated 1 day ago by
Ram
44k • written 2 days ago by
avelarbio46
▴ 30
0
votes
1
reply
141
views
Small secondary peak for per sequence GC content - FASTQC results (bulk RNA-seq)
RNAseq
updated 2 days ago by
GenoMax
142k • written 2 days ago by
Fossil
• 0
1
vote
2
replies
235
views
Construction of circos plot from WGS data
WGS
Circos
1 day ago by
Anitha
▴ 10
1
vote
3
replies
230
views
Trimmomatic running but files containing purged reads are empty
fastqc
fastq
trimmomatic
updated 2 days ago by
GenoMax
142k • written 2 days ago by
Wilber0x
▴ 50
0
votes
0
replies
102
views
How to find nucleotide changes and the predicted effect when comparing two genomes
BLAST
alignment
updated 2 days ago by
Ram
44k • written 2 days ago by
Melissa
• 0
5
votes
3
replies
203
views
FastQC interpretation - 16S sequencing
interpretation
amplicon
Fastqc
16S
updated 2 days ago by
GenoMax
142k • written 2 days ago by
Christopher
▴ 10
0
votes
0
replies
114
views
Subset of ATAC-seq peaks has high variance
atac-seq
edgeR
R
normalization
2 days ago by
Tim
• 0
2
votes
6
replies
306
views
How to get the ratio of allele counts from GATK derived VCF file?
Freebayes
GATK
SNP
VCF
2 days ago by
anikcropscience
▴ 230
0
votes
0
replies
101
views
KEGG pathway enrichment analysis in Zea mays with R
KEGG
Zea-mays
R
updated 2 days ago by
Ram
44k • written 2 days ago by
letizia.ottaviani
• 0
0
votes
6
replies
275
views
from CRAM to fastq
FASTQ
WGS
CRAM
updated 2 days ago by
ATpoint
82k • written 3 days ago by
machaalani29
• 0
0
votes
0
replies
101
views
News:
Bioinformatic Analysis of Transposable Elements course
Genome-Annotation
TE
Manual-Curation
Transposable-Elements
updated 2 days ago by
Ram
44k • written 3 days ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
127
views
No output when converting transcript IDs to gene symbols
RNA-seq
updated 2 days ago by
Ram
44k • written 3 days ago by
ashkan
▴ 160
3
votes
1
reply
159
views
vg autoindex seems stuck after a week of running
vg
pangenome
updated 3 days ago by
Jouni Sirén
▴ 380 • written 3 days ago by
StevieP
▴ 10
0
votes
0
replies
110
views
MAFFT alignment report
RNA
Alignment
MAFFT
Linux
updated 2 days ago by
Ram
44k • written 3 days ago by
Ghada
• 0
0
votes
3
replies
298
views
Kraken2 Custom Database non-deterministic results
Metagenomics
kraken2
updated 3 days ago by
colindaven
6.4k • written 4 days ago by
Bjorn
• 0
0
votes
1
reply
150
views
How to get 2 seurat objects into a DEseq
Seurat
DEseq
updated 2 days ago by
Ram
44k • written 3 days ago by
He11oJe11o
• 0
0
votes
0
replies
89
views
Rescaling normalized enrichment score (NES)
heatmap
3 days ago by
CTLong
▴ 110
0
votes
3
replies
210
views
Splitting query fasta file for Diamond Blastp make the process faster?
DIAMOND
1 day ago by
kmat
• 0
0
votes
1
reply
151
views
Mapping difference with BWA
variant-calling
samtools
bam
BWA
genomics
updated 3 days ago by
ATpoint
82k • written 3 days ago by
rj.rezwan
• 0
0
votes
0
replies
102
views
Kegg Pathways to Circos
Genomics
KEGG
Circos
3 days ago by
dlera.lozano
▴ 10
0
votes
0
replies
116
views
DIFFBIND boxplot results, p value not significant
DiffBind
ChIP-seq
2 days ago by
RD
▴ 10
3
votes
6
replies
340
views
Problem in getting geo file through GEOQUERY
geoquery
Geo
updated 2 days ago by
Ram
44k • written 3 days ago by
anasjamshed
▴ 120
0
votes
1
reply
183
views
Multi-ploid data in ANGSD and NGSadmix
ancestry
diploid
haploid
admixture
updated 3 days ago by
andersdetermig
▴ 20 • written 4 days ago by
Christopher
• 0
0
votes
2
replies
383
views
transanno liftvcf "Error: length of chromosome [chr] is not equal to length in chain file. Are you using correct reference?"
liftover
transanno
3 days ago by
ezz3
• 0
1
vote
10
replies
637
views
Add stats to the plot
R
3 days ago by
Ghada
• 0
0
votes
4
replies
237
views
Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
GATK
UnifiedGenotyper
3 days ago by
shpak.max
▴ 50
2
votes
4
replies
265
views
Allele count of 2 for homoplasmic MT variants in VCF
Variant-Calling
GATK
VCF
2 days ago by
Arton
▴ 10
1
vote
3
replies
199
views
downloading chemical database from ChEMBL
ChEMBL
PyRMD
Virtual-Screening
updated 3 days ago by
GenoMax
142k • written 3 days ago by
s
• 0
0
votes
3
replies
189
views
Where are the illumina adapters on Trimmomatic take from?
rna-seq
trimmomatic
updated 3 days ago by
GenoMax
142k • written 3 days ago by
bioinfo
▴ 150
3
votes
2
replies
182
views
Multiplexing for pooled CRISPR screen sequencing
multiplex
CRISPR-screen
Illumina
2 days ago by
Tuấn Anh
• 0
2
votes
4
replies
1.2k
views
Is it possible to run CibersortX with a very small number of samples?
cibersortx
2 days ago by
Aspire
▴ 330
1
vote
3
replies
304
views
Functional enrichment analysis for unique gene IDs
RNA-SEQ
3 days ago by
Pegasus
▴ 100
117,132 results • Page
2 of 2343
Recent Votes
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
Answer: Number of non-ATCG nucleotides replaced by Salmon
Answer: Number of non-ATCG nucleotides replaced by Salmon
Answer: ComplexHeatmap - How to change fontsize of rowAnnotation
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Recent Replies
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
by
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…
Comment: Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvage
by
Brian Bushnell
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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