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1,000 results • Page
1 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
4
views
Issues with Chromosome Encoding and VCF Annotation in dbSNP Alpha Release
tabix
index
vcf
bcftools
sbSNP
2 minutes ago by
Fernando
• 0
0
votes
0
replies
10
views
Issues while running blastx
blastx
RNA_seq
14 minutes ago by
Foad
▴ 10
0
votes
1
reply
23
views
How to determine E. coli MLST (Multi Locus Sequence Typing ) from the sequencing of the PCR product of 7 housekeeping genes
MLST
phylogenetic
nanopre
updated 18 minutes ago by
Joe
21k • written 30 minutes ago by
Ralph
• 0
0
votes
0
replies
20
views
How to remove 3rd codon positions in a multiple sequence allignment?
i
1 hour ago by
francesco.degiglio
• 0
0
votes
0
replies
23
views
Classification ML model using different type of data
machine-learning
transcriptomics
R
python
biomarkers
1 hour ago by
sil_bioinfo
▴ 40
0
votes
0
replies
24
views
RNA secondary structure for GRCH38 transcriptome
dot-bracket-notation
human
RNA-secondary-structure
GRCH38
2 hours ago by
Saad Khan
▴ 420
0
votes
0
replies
33
views
Need to PrepSCTfindMarker again after subset if the original object has already been normalized?
FindMarker
Seurat
3 hours ago by
Adrian
• 0
1
vote
1
reply
76
views
GEO dataset Microarray data analysis help
microarray
NCBI
GEO
R
data
3 hours ago by
Confused_human
▴ 20
0
votes
3
replies
120
views
Microarray batch correction method suggestions
microarray
log2_normalized
batch_correction
multiple_datasets
updated 3 hours ago by
ATpoint
78k • written 6 hours ago by
Sumeet
• 0
0
votes
0
replies
47
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
10 hours ago by
Clayton
• 0
0
votes
0
replies
55
views
Enzyme commission number in ncbi Gene database
number
commission
enzyme
10 hours ago by
Maatary
• 0
0
votes
1
reply
102
views
Java error while running HiCDC overview code
R
Juicer
HiC
HiCDCPlus
updated 12 hours ago by
Brian Bushnell
20k • written 16 hours ago by
isMM
• 0
0
votes
0
replies
61
views
error when installing gistic2 using conda
env
gistic2
conda
16 hours ago by
luckyday1661
• 0
0
votes
0
replies
70
views
Expression differs when running plotTranscripts vs boxplot of FPKM or coverage values (R)?
R
updated 16 hours ago by
Ram
41k • written 16 hours ago by
boone5jones
• 0
0
votes
0
replies
58
views
Differing output: vcftools' --weir-fst-pop and R hierfstats package's varcomp.glob()
vcftools
hierfstats
fst
16 hours ago by
S
• 0
0
votes
2
replies
158
views
what should I do if I get a compromised sample of scRNA-seq data?
scRNA-seq
data
snRNA-seq
updated 4 hours ago by
ATpoint
78k • written 19 hours ago by
wangjb702
• 0
0
votes
0
replies
67
views
Comparing 16S rRNA (culture) sequences with metagenome
metagenome
shotgun
rRNA_culture
16S
updated 19 hours ago by
Ram
41k • written 19 hours ago by
aswin
• 0
0
votes
2
replies
140
views
Filling gaps in BAM file
bamtools
samtools
gene
bam
19 hours ago by
hemr3
• 0
0
votes
1
reply
120
views
Annotation GTF/GFF Arabidopsis thaliana
Arabidopsis
GFF
GTF
Annotation
14 hours ago by
enriquesan
• 0
0
votes
0
replies
65
views
How do I pick the best conditions for scATAC-Seq after a series of bulk test runs?
ATAC-seq
20 hours ago by
cyril-cros
▴ 940
0
votes
1
reply
114
views
Microbial gene coverage from blast result
gene
coverage
5 hours ago by
aanchal.yadav
• 0
0
votes
0
replies
70
views
extracting Uniprot IDs for Kegg pathways
mapping
uniprot
R
kegg
clusterprofiler
22 hours ago by
Assa Yeroslaviz
★ 1.8k
0
votes
1
reply
87
views
Funannotate iprscan Creates empty file
funannotate
interproscan
fungus
annotation
1 day ago by
Umer
▴ 50
0
votes
2
replies
142
views
An issue with gtf file (ballgownrsem)
Ballgown
RNA-seq
GTF
RSEM
updated 1 day ago by
rpolicastro
12k • written 1 day ago by
cucindarko51
• 0
2
votes
2
replies
169
views
4 Fastq files for a single run generated by 10X
scRNA-Seq
Fastq
SRA
10X
4 hours ago by
hkarakurt
▴ 180
0
votes
3
replies
554
views
How to resolve the error of protein lacking a stop codon when using GenomeThreader for homology prediction?
genome
threader
updated 1 hour ago by
dthorbur
▴ 890 • written 1 day ago by
peanut
• 0
2
votes
5
replies
217
views
kallisto index build difference according to version
index
version
kallisto
updated 1 day ago by
dsull
★ 5.1k • written 1 day ago by
estilo
• 0
0
votes
2
replies
509
views
Understanding gene level copy number data from TCGAbiolinks
CNV
TCGA
updated 1 day ago by
Zhenyu Zhang
★ 1.1k • written 13 months ago by
billyK
• 0
1
vote
3
replies
318
views
Bam files generated with STAR cause a segmentation fault core dump error when used with another tool
RNA-Seq
mapping
updated 1 day ago by
GenoMax
136k • written 1 day ago by
bkffadia
• 0
0
votes
2
replies
200
views
RNA seq
Differential-gene-expression
updated 20 hours ago by
Ram
41k • written 1 day ago by
Byonkesh
• 0
0
votes
0
replies
108
views
Should I perform eQTL colocalization for just one of eGenes at a time?
colocalization
coloc
eCaviar
eQTL
2 days ago by
maximal_life
▴ 20
3
votes
1
reply
201
views
KEGG DATABASE
DATABASE
KEGG
updated 2 days ago by
Mensur Dlakic
★ 25k • written 2 days ago by
Sijjil
• 0
0
votes
1
reply
207
views
Issue with genetic QC sex check
plink
3 days ago by
kl
▴ 10
0
votes
0
replies
107
views
BioSQL Unable to remove database using server.remove_database
BioSQL
biopython
Mysql
Python
3 days ago by
Navindu
• 0
0
votes
0
replies
118
views
bootstraped treemix show no migration event
Treemix
Bootstrap
3 days ago by
reza
▴ 300
0
votes
2
replies
1.5k
views
Does GNOMAD use all LOFTEE LoF filters?
loftee
gnomad
LOF
ensembl
vep
updated 3 days ago by
AMARU
• 0 • written 3.8 years ago by
brismiller
▴ 50
0
votes
3
replies
806
views
"MethylKit" package for WGBS data
MethylKit
WGBS
updated 3 days ago by
viveksomya123
• 0 • written 2.3 years ago by
shrinka.genetics
▴ 20
0
votes
0
replies
140
views
is there a way to set colors pallets for glMDSPlot(x)?
Glimma
glMDSPlot
3 days ago by
James
• 0
0
votes
0
replies
128
views
Compute matrix skipping many regions stating not found in compute matrix output
computematrix
Deeptools
3 days ago by
Mehwish
▴ 10
0
votes
0
replies
196
views
How to find promoters (such as GC box and TATA box) in set of genes using bioinformatics analysis ?
promoter
motif
updated 21 hours ago by
Ram
41k • written 3 days ago by
shome
▴ 10
0
votes
3
replies
330
views
Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-voom
RNAseq
differential-gene-expession
limma
batch-effect
updated 1 day ago by
CTLong
▴ 20 • written 3 days ago by
fluke
• 0
0
votes
2
replies
237
views
How to identify CG, CHG, or CHH from MeDIP data
MethylationStudy
CHG
CHH
CG
MeDIP
1 day ago by
Tm
★ 1.1k
0
votes
0
replies
152
views
Significance of several BUSCO target IDs for the same gene
target_id
sequence-ontology
BUSCO
duplication
3 days ago by
CoLa
• 0
0
votes
1
reply
196
views
doubt about usage of megahit
trinity
megahit
updated 3 days ago by
Istvan Albert
99k • written 4 days ago by
meera
• 0
0
votes
0
replies
141
views
Osmotic permeability of water transport in aquaporins
permeability
Osmotic
transport
Water
4 days ago by
Peerzada
• 0
0
votes
1
reply
445
views
Loftee no splice site annotations
Loftee
VEP
updated 4 days ago by
AMARU
• 0 • written 21 months ago by
Filago
▴ 90
0
votes
0
replies
125
views
how to download the VCF/MAF files from cBioportal genie site
cBioportal
mutation
VCF
TMB
4 days ago by
luckyday1661
• 0
0
votes
1
reply
168
views
How to get multiple protein domain database domain name from id's
annotations
blast2go
domain
domains
proteins
updated 4 days ago by
GenoMax
136k • written 4 days ago by
Nicolas
• 0
0
votes
0
replies
141
views
Extract upstream and downstream 50bp nontemplated sequences from a position
search
sequences
nontemplated
motif
4 days ago by
Ty
• 0
0
votes
1
reply
187
views
Annotate Unplaced Scaffold with Chromosome Information
assembly
annotation
scaffold
Chromosome
updated 4 days ago by
cmdcolin
★ 3.4k • written 4 days ago by
Trevor
• 0
1,000 results • Page
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Recent Votes
Answer: BBtools bug in reporting the number of substitutions in the console output, it s
Comment: best BLAST hits - which criteria is more important?
Answer: Can't do runPCA after merging a splited Seurat object before UMAP
Answer: Can't do runPCA after merging a splited Seurat object before UMAP
Answer: RNA-seq log2 fold change to linear
Answer: RNA-seq log2 fold change to linear
Comment: How to download multiple genome files using command line (MacOS) using datasets
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▴ 50
Teacher
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3.0k
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5.8k
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Recent Replies
Comment: Problems separating and converting molecule files with openbabel
by
mthm
▴ 50
Is your problem solved? if not, what is your command?
Comment: How to determine E. coli MLST (Multi Locus Sequence Typing ) from the sequencing
by
Joe
21k
Give the sequences to an MLST server or commandline tool on a per-sample/isolate basis. The tool will specify the format it wants - probab…
Answer: contrast file in DESeq2 bioconductor
by
r.shiasi3897
▴ 10
Thank you very much. i will try it
Answer: Best method for batch correction of three datasets
by
ATpoint
78k
Datasets 1 and 2 have nothing in common to serve as batch correction "anchor" (literally speaking), so you cannot correct for anything here…
Answer: contrast file in DESeq2 bioconductor
by
ATpoint
78k
What do you want to compare? 1) You can compare pairwise, like TS vs EOT and TS vs FU and EOT vs FU. That would be ```r results(dds, c…
Comment: How to resolve the error of protein lacking a stop codon when using GenomeThread
by
dthorbur
▴ 890
Ah, there is nothing in your post to suggest you are looking for a specific parameter to ignore a specific warning. I would suggest you edi…
Comment: How to download multiple genome files using command line (MacOS) using datasets
by
GenoMax
136k
You can use ./datasets download genome accession --inputfile file_name_w_accession `file_name_w_accession` should contain one access…
Comment: How to download multiple genome files using command line (MacOS) using datasets
by
Michael
53k
here https://stackoverflow.com/a/1521498 is an example how to use read and for loop, you just need to put in your command.
Answer: How to download multiple genome files using command line (MacOS) using datasets
by
Michael
53k
datasets download genome accession --inputfile accessions.txt --include gff3,gbff,rna,cds,protein,genome,seq-report ---------- Or you…
Comment: GEO dataset Microarray data analysis help
by
Basti
★ 1.9k
First I advise you to take time to correctly edit your post so that your code is readable. Secondly, you provide a lot of irrelevant code l…
Comment: How to download multiple genome files using command line (MacOS) using datasets
by
scholaraspect2008
• 0
hi there, thanks for the reply, is it possible to disclose an example of ./datasets script for that? thank you very much. i m currently try…
Comment: How to download multiple genome files using command line (MacOS) using datasets
by
Michael
53k
> you can use the commands of curl , wget and slow5curl to download the data from database. Not in this situation, it is much easier to us…
Comment: Microarray batch correction method suggestions
by
ATpoint
78k
Makes no sense in my opinion. It's different experiments that cannot be quantitatively compared.
Comment: How to download multiple genome files using command line (MacOS) using datasets
by
scholaraspect2008
• 0
by means of that, how should i write my scripting? say i have GCF000001 GCF000002 GCF000003 btw sorry if i wasn't that clear with the …
Comment: 4 Fastq files for a single run generated by 10X
by
hkarakurt
▴ 180
Thank you for your detailed answer. I will check the reads and compare them with chemistry manual as you suggested. Thank you again for yo…
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