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1,000 results • Page
1 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
1
reply
7
views
Very low successfully assigned alignments with feature counts
RNAseq
featureCounts
just now by
Manuel
• 0
0
votes
4
replies
145
views
Need help to find FASTA sequence from dbSNP
dbSNP
SNP
FASTA
updated 35 minutes ago by
GenoMax
136k • written 6 hours ago by
syedahumairagillani
• 0
0
votes
0
replies
48
views
ASEReadCounter output wrong number of coverage
ASEReadCounter
8 hours ago by
junhuili
• 0
1
vote
1
reply
987
views
How to interpret the discrepancy of assignment rate in featurecounts using forward and reverse strand protocols
RNAseq
updated 8 hours ago by
charles.feigin
• 0 • written 6 weeks ago by
xinrantian
▴ 20
0
votes
0
replies
55
views
megablast taxonomy assign in blobtools
blobtools
11 hours ago by
bs
• 0
0
votes
0
replies
68
views
Aligning sequences with multiple genetic codes!
genetic_codes
codon
MEGA11
alignment
14 hours ago by
George X.
• 0
0
votes
1
reply
104
views
Cell ranger multi for demultiplexing FB files and GEX files
ranger
multi
cell
updated 11 hours ago by
GenoMax
136k • written 15 hours ago by
Shloka
• 0
0
votes
0
replies
64
views
Ambient RNA removal method that generates whole (integer) counts
pseudobulk
soupX
DESeq2
single-cell
17 hours ago by
EK
• 0
0
votes
1
reply
109
views
Software for Spatial Transcriptomic data [NanoString; Visium]?
NanoString
Visium
Spatial-Transcriptomics
10X
12 hours ago by
LauferVA
3.8k
1
vote
1
reply
107
views
ANNOVAR Download Failing
ANNOVAR
updated 17 hours ago by
Ram
41k • written 19 hours ago by
tony
• 0
0
votes
1
reply
116
views
Sorted bam files are empty after sorting them from bam
bam
dna
updated 17 hours ago by
Ram
41k • written 19 hours ago by
mgranada3
▴ 30
0
votes
2
replies
163
views
Downsampling ATAC-seq BAM files
ATAC-seq
16 hours ago by
Elise
• 0
0
votes
0
replies
66
views
spatial metabolomics, python
spatial-metabolomics
updated 20 hours ago by
Ram
41k • written 20 hours ago by
joha
▴ 10
1
vote
4
replies
179
views
Feasibility of Enrichment Analysis from RTqPCR results
GO
RT-qPCR
Enrichment-Analysis
updated 8 hours ago by
GenoMax
136k • written 23 hours ago by
Javier
• 0
0
votes
0
replies
82
views
WGCNA for different tissues
WGCNA
Worms
RNA-Seq
23 hours ago by
kdca
• 0
0
votes
1
reply
142
views
Contrasts in R
contrasts
r
updated 21 hours ago by
jv
★ 1.3k • written 1 day ago by
SGMS
▴ 130
0
votes
1
reply
323
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 1 day ago by
Joe
21k • written 1 day ago by
Ralph
• 0
0
votes
1
reply
127
views
How to remove 3rd codon positions in a multiple sequence allignment?
i
updated 21 hours ago by
Ram
41k • written 1 day ago by
francesco.degiglio
• 0
0
votes
0
replies
87
views
Classification ML model using different type of data
machine-learning
transcriptomics
R
python
biomarkers
1 day ago by
sil_bioinfo
▴ 40
0
votes
0
replies
76
views
RNA secondary structure for GRCH38 transcriptome
dot-bracket-notation
human
RNA-secondary-structure
GRCH38
1 day ago by
Saad Khan
▴ 420
0
votes
0
replies
73
views
Need to PrepSCTfindMarker again after subset if the original object has already been normalized?
FindMarker
Seurat
1 day ago by
Adrian
• 0
3
votes
1
reply
133
views
GEO dataset Microarray data analysis help
R
microarray
NCBI
GEO
updated 21 hours ago by
Ram
41k • written 1 day ago by
Confused_human
▴ 20
0
votes
3
replies
178
views
Microarray batch correction method suggestions
microarray
batch-correction
updated 17 hours ago by
Ram
41k • written 1 day ago by
Sumeet
• 0
0
votes
0
replies
85
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
1 day ago by
Clayton
• 0
0
votes
0
replies
90
views
Enzyme commission number in ncbi Gene database
enzyme-commission-number
updated 21 hours ago by
Ram
41k • written 1 day ago by
Maatary
• 0
0
votes
1
reply
142
views
Java error while running HiCDC overview code
R
Juicer
HiC
HiCDCPlus
updated 1 day ago by
Brian Bushnell
20k • written 1 day ago by
isMM
• 0
2
votes
4
replies
249
views
error when installing gistic2 using conda
conda
gistic2
updated 17 hours ago by
Ram
41k • written 1 day ago by
luckyday1661
• 0
0
votes
0
replies
107
views
Expression differs when running plotTranscripts vs boxplot of FPKM or coverage values (R)?
R
updated 1 day ago by
Ram
41k • written 1 day ago by
boone5jones
• 0
0
votes
0
replies
92
views
Differing output: vcftools' --weir-fst-pop and R hierfstats package's varcomp.glob()
vcftools
hierfstats
fst
1 day ago by
S
• 0
0
votes
2
replies
195
views
what should I do if I get a compromised sample of scRNA-seq data?
scRNA-seq
data
snRNA-seq
updated 1 day ago by
ATpoint
78k • written 1 day ago by
wangjb702
• 0
0
votes
0
replies
90
views
Comparing 16S rRNA (culture) sequences with metagenome
metagenome
shotgun
rRNA_culture
16S
updated 1 day ago by
Ram
41k • written 1 day ago by
aswin
• 0
0
votes
4
replies
255
views
Filling gaps in BAM file
bamtools
samtools
gene
bam
updated 17 hours ago by
seidel
11k • written 1 day ago by
hemr3
• 0
0
votes
1
reply
139
views
Annotation GTF/GFF Arabidopsis thaliana
Arabidopsis
GFF
GTF
Annotation
1 day ago by
enriquesan
• 0
0
votes
0
replies
79
views
How do I pick the best conditions for scATAC-Seq after a series of bulk test runs?
ATAC-seq
1 day ago by
cyril-cros
▴ 940
0
votes
1
reply
133
views
Microbial gene coverage from blast result
gene
coverage
1 day ago by
aanchal.yadav
• 0
0
votes
0
replies
84
views
extracting Uniprot IDs for Kegg pathways
mapping
uniprot
R
kegg
clusterprofiler
2 days ago by
Assa Yeroslaviz
★ 1.8k
0
votes
1
reply
98
views
Funannotate iprscan Creates empty file
funannotate
interproscan
fungus
annotation
2 days ago by
Umer
▴ 50
1
vote
3
replies
191
views
An issue with gtf file (ballgownrsem)
Ballgown
RNA-seq
GTF
RSEM
3 hours ago by
cucindarko51
• 0
2
votes
2
replies
201
views
4 Fastq files for a single run generated by 10X
scRNA-Seq
Fastq
SRA
10X
1 day ago by
hkarakurt
▴ 180
0
votes
4
replies
639
views
How to resolve the error of protein lacking a stop codon when using GenomeThreader for homology prediction?
genome
threader
12 hours ago by
peanut
• 0
2
votes
5
replies
226
views
kallisto index build difference according to version
index
version
kallisto
updated 2 days ago by
dsull
★ 5.1k • written 2 days ago by
estilo
• 0
0
votes
2
replies
514
views
Understanding gene level copy number data from TCGAbiolinks
CNV
TCGA
updated 2 days ago by
Zhenyu Zhang
★ 1.1k • written 13 months ago by
billyK
• 0
1
vote
3
replies
329
views
Bam files generated with STAR cause a segmentation fault core dump error when used with another tool
RNA-Seq
mapping
updated 2 days ago by
GenoMax
136k • written 2 days ago by
bkffadia
• 0
0
votes
0
replies
112
views
Should I perform eQTL colocalization for just one of eGenes at a time?
colocalization
coloc
eCaviar
eQTL
3 days ago by
maximal_life
▴ 20
4
votes
2
replies
265
views
KEGG DATABASE
DATABASE
KEGG
updated 21 hours ago by
jv
★ 1.3k • written 3 days ago by
Sijjil
• 0
0
votes
1
reply
212
views
Issue with genetic QC sex check
plink
4 days ago by
kl
▴ 10
0
votes
0
replies
111
views
BioSQL Unable to remove database using server.remove_database
BioSQL
biopython
Mysql
Python
4 days ago by
Navindu
• 0
0
votes
0
replies
124
views
bootstraped treemix show no migration event
Treemix
Bootstrap
4 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 4 days ago by
AMARU
• 0 • written 3.8 years ago by
brismiller
▴ 50
0
votes
3
replies
809
views
"MethylKit" package for WGBS data
MethylKit
WGBS
updated 4 days ago by
viveksomya123
• 0 • written 2.3 years ago by
shrinka.genetics
▴ 20
1,000 results • Page
1 of 20
Recent Votes
scRNA-seq CITE-seq-count bioinformatics
Comment: Can you help me to download list of miRNA from a SRA under a bioproject ?
Comment: Can you help me to download list of miRNA from a SRA under a bioproject ?
A: problem with chromosomes in michigan imputation server
Answer: Execute R command on specific termimal
rRNA decontamination of RNA-Seq reads (tool choice, introns etc)
Answer: Calculate GC content for entire chromosome
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Recent Replies
Comment: Very low successfully assigned alignments with feature counts
by
GenoMax
136k
Is the genome/annotation from the same source i.e. Ensembl or so it appears?
Comment: Calculate GC content for entire chromosome
by
ATpoint
78k
What does this do? It's not documented well and does not work for me in terms of, it produces no output: cat foo.fa >chr1 GCGC…
Comment: Need help to find FASTA sequence from dbSNP
by
GenoMax
136k
Did you not see the last part in my comment above about how to get the sequence?
Comment: Execute R command on specific termimal
by
QX
• 0
Hi @atpoint Thank you for your answer!
Comment: Need help to find FASTA sequence from dbSNP
by
syedahumairagillani
• 0
Thank you for your response. Actually I am looking for fasta sequence of SNP as I shared via image, rather than just location. Would you p…
Answer: Calculate GC content for entire chromosome
by
colindaven
5.8k
In the meantime there is also seqtk gc https://github.com/lh3/seqtk seqtk gc Usage: seqtk gc [options] <in.fa> …
Comment: Building reference dbSNP file using WGS samples
by
analyst
▴ 10
I have employed your above suggested approach for BQSR (latter one). I will try former approach too (that does not require reference vcf fi…
Comment: An issue with gtf file (ballgownrsem)
by
cucindarko51
• 0
Thank you! After using this tool, I figured out that **ballgownrsem** can be run successfully only with GFF files.
Answer: Execute R command on specific termimal
by
ATpoint
78k
This is not how HPCs work. Things do not happen automatically and independent of the job scheduler. If you want to work interactively o…
Comment: Need help to find FASTA sequence from dbSNP
by
GenoMax
136k
Using [**EntrezDirect**][1] you can find the location of this SNP: $ esearch -db snp -query rs1815739 | esummary | xtract -pattern Doc…
Comment: Building reference dbSNP file using WGS samples
by
analyst
▴ 10
For variant calling I followed following steps: **Step 1** I first made a vcf file to be used for quality score recalibration later > c…
Comment: Need help to find FASTA sequence from dbSNP
by
Pierre Lindenbaum
158k
what does it mean ?
Answer: How to use Nextflow to call scripts from different environments?
by
ATpoint
78k
You can specify conda environments and containers directly in the modules, see for example: https://github.com/nf-core/modules/blob/master…
Comment: Issues while running blastx
by
GenoMax
136k
> ~/Downloads/uniprot_sprot.dat `dat` files are not blast index ready. You should download the `fasta` format file and create your own bla…
Comment: Strandedness of RNA-seq results
by
charles.feigin
• 0
Hi, coming here for the same reason. Libraries prepared with the Illumina Stranded mRNA Prep kit (dUTP-based). In hisat2 with --rf I get <…
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