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336 results • Page
3 of 7
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
97
views
GMT file from eggnog annotation
gmt
annotation
Eggnog
8 days ago by
jorge.cortes.miranda
• 0
1
vote
2
replies
226
views
How can I amend the output of a DIAMOND python script?
Python
Diamond
COG_analysis
8 days ago by
eamaunders
• 0
1
vote
2
replies
250
views
Problem in installing 'magick' R package
R
installation
package
magick
updated 9 days ago by
DBScan
▴ 210 • written 9 days ago by
applepie
• 0
0
votes
3
replies
291
views
Viral genes not showing up in combined mouse+virus alignment
RNAseq
8 days ago by
cook.675
▴ 210
1
vote
5
replies
383
views
CHIPSEQ : Cut AND Run , DiffBind Parameters
Cut-Run
DiffBind
ChIP-seq
updated 22 hours ago by
Rory Stark
★ 2.0k • written 9 days ago by
DINESHR
• 0
0
votes
0
replies
118
views
MUSCLE Protein Alignment of Distantly Related Proteins
muscle
protein
alignment
9 days ago by
Richard Fontaine
• 0
4
votes
6
replies
452
views
bwa mem hangs after a few thousand reads
bwa-mem
alignment
bwa
calling
variant
8 days ago by
cee28
▴ 30
2
votes
2
replies
832
views
Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when pivoting from wide to long format
rnaseq
pivot_longer
ggplot2
updated 9 days ago by
cmdcolin
★ 3.4k • written 9 days ago by
Dylan C-C
• 0
3
votes
4
replies
340
views
Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not present in R
FDR
volcano
plotting
R
plot
updated 9 days ago by
Nitin Narwade
★ 1.5k • written 9 days ago by
RNAseqer
▴ 250
0
votes
0
replies
123
views
scVelo cell transitions from marker gene expressing cells
velocity
scvelo
RNA
9 days ago by
rbronste
▴ 420
1
vote
3
replies
288
views
Identify clusters of populations based on gene expression
Seq
Single
cell
RNA
updated 9 days ago by
Nitin Narwade
★ 1.5k • written 10 days ago by
Bine
▴ 50
0
votes
1
reply
175
views
Python function to export the annotated records to genbank file using python and biopython
biopython
python
bioinformatic
programming
updated 9 days ago by
barslmn
★ 2.0k • written 10 days ago by
Saurabh
• 0
1
vote
6
replies
387
views
Discrepancy in total number of bases in trimmed read1 and read2 files after BBDuk
bbduk
9 days ago by
CTLong
▴ 30
2
votes
1
reply
169
views
unicycler error : [Errno 13] Permission denied:
unicycler
updated 9 days ago by
barslmn
★ 2.0k • written 10 days ago by
jiyoung
▴ 20
0
votes
0
replies
110
views
Does breadth of coverage signify expression?
Coverage
breadth
Bedtools
Expression
count
10 days ago by
Smriti
▴ 10
1
vote
4
replies
296
views
Bowtie mapping for single_end read
bowtie
9 days ago by
Rita
• 0
0
votes
0
replies
118
views
missing region in the process of annotation
annotatr
minfi
10 days ago by
Aki
▴ 10
1
vote
0
replies
108
views
Visualize and explore eventalign data against reference
igv
minimap
nanopolish
nanopore
ngs
10 days ago by
joe
▴ 420
0
votes
6
replies
406
views
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
RNA-Seq
Nanopore
ONT
differential
expression
8 days ago by
tw_140
• 0
9
votes
15
replies
858
views
Construction of single sequence assembly out of contigs
Contigs
Bacteria
Genome
WGS
9 days ago by
analyst
▴ 10
0
votes
0
replies
106
views
Differentiate sequenced and imputed variants in BGEN files
imputation
bgen
ukb
11 days ago by
user230613
▴ 350
0
votes
4
replies
287
views
Species coverage in the NCBI protein NR database ?
NR
updated 10 days ago by
Istvan Albert
99k • written 11 days ago by
HERMAN
▴ 10
0
votes
0
replies
115
views
addPatternDensity to qsea object
maxDensityPattern
medip
qsea
11 days ago by
Jaykishan
• 0
1
vote
1
reply
181
views
Harmony integration PC variance explained
scRNA
integration
harmony
updated 9 days ago by
CTLong
▴ 30 • written 11 days ago by
e.iich
• 0
0
votes
3
replies
262
views
merged rs number information
merged
dbsnp
10 days ago by
sskimvd
• 0
1
vote
1
reply
175
views
Beginner differential methylation analysis
Methylation
updated 11 days ago by
Basti
★ 1.9k • written 11 days ago by
a.basitkhan1990
▴ 30
2
votes
1
reply
253
views
EnhancedVolcano underrepresenting DEGs
R
updated 9 days ago by
Kevin Blighe
86k • written 11 days ago by
jabbari.parnian
▴ 30
0
votes
0
replies
119
views
[maftools]Too many multi_hit and missense mutation
maftools
gatk
MAF
data
WES
VCF
11 days ago by
jiazheng_lin
• 0
0
votes
0
replies
134
views
Negative F statistics for sex check in plink
plink
check
sex
11 days ago by
kl
▴ 10
0
votes
1
reply
205
views
Chipseq peak calling and peak frequency region
chipseeker
macs2
updated 10 days ago by
Arup Ghosh
3.2k • written 12 days ago by
Mehwish
▴ 10
0
votes
1
reply
265
views
issue in RNA -seq analysis
NGS
RNA-Seq
updated 13 days ago by
GenoMax
136k • written 13 days ago by
subhiksha
• 0
0
votes
3
replies
373
views
Alternatives to Music2 for rnaseq deconvolution without disease scRNA dataset
scRNA
deconvolution
Music
Music2
bulk
updated 13 days ago by
ATpoint
78k • written 13 days ago by
manuelmourato25
• 0
0
votes
3
replies
321
views
Annovar - Annotated file cells show string
annovar
13 days ago by
Roshan
• 0
0
votes
1
reply
271
views
MinKNOW software installation doubt for MinION Nanopore sequencing
MinKNOW
MinION
Nanopore
updated 13 days ago by
GenoMax
136k • written 13 days ago by
Soumajit
▴ 40
0
votes
1
reply
233
views
htShinyExample-5.3 - not working
htShiny
Oncoprint
InteractiveComplexHeatmap
updated 8 days ago by
Ram
41k • written 13 days ago by
bioinfo
▴ 60
0
votes
3
replies
288
views
labelling the clusters from the CD4 T cell scRNAseq data
scRNAseq
14 days ago by
Sara
▴ 230
0
votes
0
replies
889
views
Any tools for finding the telomere sequences / lengths directly for nanopore sequencing reads without any prior knowledge of the organism
genomics
telomeres
reads
14 days ago by
Mark
• 0
0
votes
0
replies
162
views
not best k value found
de
assemblly
assembly
novo
kmergenie
14 days ago by
shaileshdesai76
• 0
0
votes
0
replies
172
views
Multi-mapped reads in Ribo-Seq data, discard or keep?
STAR
ribo-seq
multi-mapped
rna-seq
TE
14 days ago by
Carmen
• 0
0
votes
0
replies
175
views
Identifying differentially expressed loci for gene duplicates using DESeq2
rna-seq
deseq2
14 days ago by
pl23
• 0
0
votes
2
replies
297
views
Find Genes in Homer Analysis that have the enriched Motif
single
ORA
nucleus
mRNA
Homer
10 days ago by
je71xusa
• 0
0
votes
2
replies
289
views
Tool to get genes in the neighbourhood of a particular gene
locus
Gene
updated 14 days ago by
Raony Guimarães
★ 1.3k • written 14 days ago by
ThePlaintiff
▴ 80
2
votes
9
replies
699
views
Salmon (or other pseudo-mappers) for multi-species RNAseq read filtering
STAR
Salmon
mapper
aligner
RNAseq
8 days ago by
ian.will
▴ 10
5
votes
2
replies
258
views
RNA Contamination Tool for Developing Cell Samples
contamination
scRNA
quality
RNA
SoupX
13 days ago by
Rafael Soler
★ 1.2k
1
vote
2
replies
212
views
DOES MGI SEQUENCING RESULT CONTAINS MULTIPLE FILES FOR SINGLE SAMPLE
whole
genome
assembly
sequencing
updated 15 days ago by
WouterDeCoster
47k • written 15 days ago by
manaswiniparija3
▴ 10
1
vote
0
replies
144
views
What are the methods to correlate/study metabolomics data to proteomics data?
metabolomics
proteomics
multiomics
15 days ago by
WUSCHEL
▴ 720
0
votes
3
replies
326
views
R ComplexHeatmap - Dividing Column Annotation into Distinct Y-Axis Scales
R
complexheatmap
updated 9 days ago by
jv
★ 1.3k • written 15 days ago by
TC_Chang
▴ 10
0
votes
0
replies
120
views
Find equivalent pathways between KEGG, Reactome, and WikiPathways
pathway
mapping
database
15 days ago by
Ngrin
• 0
0
votes
0
replies
134
views
GenAlEx Haploid Data Detecting Recombination
GenAlEx
Popgen
Haploid
Recombination
15 days ago by
turcoa1
• 0
0
votes
0
replies
137
views
TF Footprinting using HINT ATAC module from RGT
hintatac
footprinting
rgttoolbox
atacseq
15 days ago by
alphaflylizard
• 0
336 results • Page
3 of 7
Recent Votes
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out
Answer: How to query 1000 genomes project VCF files for specific regions without downloa
Answer: Issue softclipping reads when they belong and don't belong to a common amplicon
Answer: Issue softclipping reads when they belong and don't belong to a common amplicon
Answer: how to remove multiple columns from a file in R
Answer: how to remove multiple columns from a file in R
Answer: Read count vs Depth
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Comment: Normalization of RNA captureSeq data (<20 genes captured)
by
ATpoint
78k
What is the question exactly? With only 20 genes you basically **must** use the spike-ins as that few genes do not really allow to normaliz…
Comment: Building reference dbSNP file using WGS samples
by
analyst
▴ 10
Dear [Brian][1] I realized that problem is with callvariants.sh script because when I called variants using freebayes I did not find aforem…
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out
by
analyst
▴ 10
Its bbmap tool callvariants.sh. I think you are right because I did not get such error when I called variants through freebayes.
Answer: Efficient way of calculating the number of mismatches between two sets of sequen
by
j.gleixner
• 0
Since all your sequences have the same length (say M) and you are only looking concerned with hamming distance you can encode your sequence…
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by
GenoMax
136k
ChatGPT says Disease Prevalence Approximate Number of Cases (Worldwide) Cardiovascular Diseases High Over 17 million deaths annual…
Comment: Where to download excel file to include major human disease, prevalence and inci
by
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158k
using wikidata: https://query.wikidata.org/sparql?query=%0ASELECT%20%3Fitem%20%3FitemLabel%20%3FitemDescription%20%3Fprevalence%20%3Fdoid%0…
Comment: Opinion on miRNA pipeline
by
ju_ra
• 0
Thank you very much! I see you decided to go for Bowtie as aligner. Do you see any issue in using STAR (as a splice aware reader technicall…
Answer: How to avoid missannotated GO terms?
by
Elisabeth Gasteiger
★ 2.3k
Please contact the UniProt helpdesk whenever you find such annotations, especially in these cases where the GO evidence/source tag says "Un…
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out
by
Pierre Lindenbaum
158k
again, it's a problem with the variant caller, which is ?
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out
by
analyst
▴ 10
Not only opposite case but same case nucleotides are also present in vcf fle. ![enter image description here][1] [1]: /media/images/4…
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out
by
analyst
▴ 10
Yes [Pierre][1] there is lower case **g** in **REF** and upper case **G** in **ALT** field. My question is that why variant caller is calli…
Answer: gatk SelectVariants is giving error while extracting SNPs out of vcf file
by
Pierre Lindenbaum
158k
This is an error in your input vcf file. The REF allele MUST be différent from the ALT allele.
Comment: gatk SelectVariants is giving error while extracting SNPs out of vcf file
by
analyst
▴ 10
I observed that my reference genomic fasta file contains both lower case and upper case nucleotides. Do I need to convert lower case nucle…
Comment: Building reference dbSNP file using WGS samples
by
analyst
▴ 10
I observed that both lower and upper cases are present in reference fasta file. Is bbtool case sensitive that while calling variants it con…
Comment: Read count vs Depth
by
Mary
• 0
Thanks Brain Bushnell Referring to my query1: So u mean that for a particular gene, if total read count is 6, then depth may be just 1 or …
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