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1,000 results • Page
4 of 20
Sort: Rank
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Votes
Replies
0
votes
0
replies
110
views
RNA velocity after SoupX in single cell data
soupX
scrna
transcriptomics
nuclei
updated 11 days ago by
GenoMax
141k • written 11 days ago by
shersky
• 0
0
votes
0
replies
106
views
What is more important for Structural Variant Calling? Recall or Precision?
structural-variants
merging
precision-recall
11 days ago by
Luke
• 0
1
vote
1
reply
447
views
PLINK multivariable GLM output: p-value without BETA and SE
linear-model
glm
plink
updated 11 days ago by
chrchang523
10k • written 11 days ago by
dsbusiness135
▴ 10
1
vote
2
replies
194
views
In need of help with my RNA velocity trajectory inference pipeline!
RNAvelocity
11 days ago by
phhelou5
• 0
0
votes
1
reply
258
views
How to do further funtional analysis of DEG KeggGet output list?
KEGGREST
DESEQ2
RNA-Seq
DEG
11 days ago by
joana.maclean
• 0
8
votes
10
replies
666
views
bash script
whole-genome-sequencing
updated 4 days ago by
Ram
43k • written 11 days ago by
bestone
▴ 30
0
votes
0
replies
112
views
Confusion with somatic variant calling: Advice on Ensembl-compatible resources?
GATK
Mutect2
ensembl
10 days ago by
DGTool
• 0
1
vote
1
reply
159
views
permutation test in edgeR
rna-seq
edgeR
updated 11 days ago by
dariober
14k • written 11 days ago by
Netanel
• 0
0
votes
0
replies
266
views
Different rsID for the same chromsome, position, ref & alt allele depending on different data sources. Which one should I use?
UKB
rsID
UKB-PPP
ensembl-vep
dbsnp
9 days ago by
lsy9
▴ 20
0
votes
0
replies
124
views
How can I plot the PCA with the raw count mRNA seq data?
PCA
normalization
updated 11 days ago by
Ram
43k • written 12 days ago by
Yoomi
▴ 20
0
votes
0
replies
112
views
Blast2GO Fisher test
Fisher-test
Go-annotation
Blast2GO
updated 11 days ago by
Ram
43k • written 12 days ago by
BlackM
• 0
0
votes
1
reply
160
views
How do I run fastq-dump on multiple prefetched files at once?
sratoolkit
fastq-dump
updated 12 days ago by
Pierre Lindenbaum
161k • written 12 days ago by
biotrekker
▴ 100
0
votes
2
replies
255
views
Regions not clear in VCF
whole-exome
variant-calling
updated 11 days ago by
Ram
43k • written 12 days ago by
priya.bmg
▴ 60
0
votes
0
replies
132
views
NA values showing at duplicacy removal step
Microarray
RNA-Seq
12 days ago by
prithvi.mastermind
▴ 50
0
votes
0
replies
134
views
Comparing molecular subtypes identified by microarray or bulk RNASeq in ssRNASeq data
microarrray
single-cell
RNASeq
subtype
13 days ago by
akhattri
▴ 50
0
votes
1
reply
262
views
cibersort. problem
cibersort
gema122
updated 11 days ago by
Ram
43k • written 15 days ago by
gem1
• 0
1
vote
3
replies
375
views
multiple sequence alignment
BLAST
multiple-sequence-alignment
clustal-omega
MSA
updated 11 days ago by
Ram
43k • written 14 days ago by
catherinemaria2728
• 0
0
votes
1
reply
208
views
Best way to add alter fastq file by adding short repeats
fastq
updated 14 days ago by
GenoMax
141k • written 14 days ago by
pairedttest
▴ 10
0
votes
0
replies
149
views
PolyA in FastQC results from EM-Seq?
fastqc
wgbs
polya
methylation
emseq
14 days ago by
Watermelon
• 0
0
votes
1
reply
204
views
POD5 files
ONT
updated 14 days ago by
GenoMax
141k • written 14 days ago by
marco.barr
▴ 60
1
vote
4
replies
339
views
How to get human-mouse conservation score from UCSC
conservation
mouse
IGV
human
score
14 days ago by
diqixiaoyaoer
▴ 10
0
votes
0
replies
154
views
Problem with GATK FilterMutectCalls : using contamination table doesn' t change anything
vcf
contaminationtable
gatk
filtermutectcalls
genomics
14 days ago by
Samuel
▴ 20
0
votes
1
reply
217
views
How do I know whether it is not a failure of ChIPseq data
ChIPseq
updated 12 days ago by
dthorbur
★ 1.9k • written 14 days ago by
Herman Einstein
• 0
0
votes
0
replies
143
views
CIBERSORT deconvolution by using long read sequencing data
long-read-sequencing
CIBERSORT
updated 14 days ago by
Ram
43k • written 14 days ago by
IVORY
• 0
0
votes
0
replies
154
views
Saccharomyces cerevisiae orthologs in plants
database
orthologs
15 days ago by
dec986
▴ 370
0
votes
0
replies
136
views
Looking for Comprehensive Virtual Screening Examples with Results Validation
drug-discovery
virtual-screening
molecular-docking
updated 15 days ago by
Ram
43k • written 15 days ago by
Stefano
• 0
0
votes
1
reply
178
views
samflags to removes mapped concordantly >1 times
samtools
Bowtie2
Metagenome
updated 8 days ago by
jkbonfield
★ 1.2k • written 15 days ago by
pompam_5904
• 0
4
votes
2
replies
213
views
Trying to write bwa mem -> samtools view -> samtools sort loop
bwa
samtools
mapping
genome
updated 15 days ago by
Pierre Lindenbaum
161k • written 15 days ago by
Lee
• 0
0
votes
0
replies
123
views
TransDecoder ORF score to filter "noise" from de novo transcriptome assembly
transdecoder
assembly
transcriptome
updated 15 days ago by
Ram
43k • written 15 days ago by
tdamiani
• 0
0
votes
0
replies
114
views
Should I keep taxa that have 0 counts when calculating alpha diversity?
Shannon-Weiner
15 days ago by
DNAngel
▴ 250
0
votes
5
replies
316
views
BUSCO analysis failed due to Duplicate of sequence in Input genome fasta. How to solve this problem ?
duplicate
BUSCO.
updated 15 days ago by
GenoMax
141k • written 15 days ago by
Sony
▴ 10
0
votes
1
reply
147
views
MMSeqs2 Removing Redundancy
mmseqs
mmseqs2
updated 15 days ago by
GenoMax
141k • written 15 days ago by
dthorbur
★ 1.9k
0
votes
0
replies
107
views
Transcription Factor Binding sites intersecting Transposable Elements
TE
TFBP
15 days ago by
M.Adiba
• 0
0
votes
5
replies
315
views
Incongruencies in GT assignment by Freebayes
depth
freebayes
heterozygous
genotype
14 days ago by
virginia.baraja
• 0
0
votes
0
replies
102
views
Extracting tcga images for cnn in r
rstudio
python
tcga-lihc
svs
15 days ago by
jain72744
▴ 10
0
votes
3
replies
206
views
Peptide identification from Mass spec data
Transcriptomics
Proteins
Mass-spec
updated 15 days ago by
Ram
43k • written 15 days ago by
atharvakarkare14
▴ 10
0
votes
7
replies
390
views
DESeq: too low p-value for RNAseq
R
DESeq
p-value
RNA-seq
FDR
updated 14 days ago by
Papyrus
★ 2.9k • written 15 days ago by
doramora
▴ 10
0
votes
0
replies
332
views
Looking to improve my understanding of Homer's mergePeaks function: unclear of how the merged file is created?
Homer
ATACseq
15 days ago by
Ronin
• 0
0
votes
0
replies
94
views
RobustRankAggreg rankMatrix subscript out of boundaries
RobustRankAggreg
microarray
R
rankMatrix
15 days ago by
hagl
▴ 10
0
votes
3
replies
262
views
How do I handle it if there are multiple ENSEMBL IDs in one gene symbol in the scRNA sequencing data?
Seurat
scRNA-seq
count-matrix
12 days ago by
Jeyong
• 0
0
votes
0
replies
84
views
Handling data from RNA-seq experiement with negative cell controls / Water samples
rnaseq
16 days ago by
kvn95ss
▴ 20
1
vote
1
reply
178
views
R/Python script to collect allele frequency for batch of SNPs in gnomAD database
gnomAD
15 days ago by
Shicheng Guo
★ 9.4k
0
votes
0
replies
99
views
Seurat-DE analysis
seurat
DE
16 days ago by
odi
▴ 10
0
votes
1
reply
144
views
sorted bam file generated from gff transcript fastas, how to get counts with HTseq?
htseq
bam
updated 16 days ago by
Ram
43k • written 16 days ago by
RNAseqer
▴ 260
1
vote
5
replies
327
views
samtools filtering
samtools
updated 8 days ago by
jkbonfield
★ 1.2k • written 16 days ago by
sansan_96
▴ 80
0
votes
0
replies
101
views
R/Python function to retrieve interacted proteins from HPA database
HPA
16 days ago by
Shicheng Guo
★ 9.4k
0
votes
0
replies
107
views
Extracting Enhancer Regions from ENCODE Annotation Files
ENCODE
enhancer
16 days ago by
YamengWu
• 0
0
votes
0
replies
97
views
Normalization approaches of RNAseq data before WGCNA
DEseq2
voom
WGCNA
16 days ago by
gimenagomez
• 0
0
votes
6
replies
438
views
Error in running Mauve alignner in Ubuntu 20.04
java
linux
aligner
mauve
10 days ago by
marongiu.luigi
▴ 710
0
votes
2
replies
213
views
RNA-Seq isoforms identification
RNA-seq
updated 16 days ago by
Andres
▴ 20 • written 16 days ago by
latita.atun
• 0
1,000 results • Page
4 of 20
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Answer: MEGA Analysis Issue on High-Performance Computer
Comment: Ciriquant not configuring hisat2 indexed files
bcftools multiple commands
bcftools pipe generated file from first command with second
C: How to setup a Summarized Experiment
A: How to download genome assemblies from NCBI with a list of GCA identifiers?
what's the genomic location and name of gene responsible for orange and black patches in calico cats
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Comment: Ciriquant not configuring hisat2 indexed files
by
Atul K.
• 0
Thank you. Decreased the threads to 2 (changed the threads: 2 in the config file; but it was somehow using 4). It did run for sometime but …
Answer: GTF file from Stringtie to R Studio for either Ballgown or DESeq2
by
Ram
43k
See this section on how to use tximport to import StringTie output for DESeq2 processing: https://bioconductor.org/packages/devel/bioc/vign…
Comment: how to find genes that are significantly expressed in brain cortex samples
by
Ram
43k
Can you explain the normalization or give me a link that describes it, please? Comparison across samples will always be caveated as RNA-seq…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
Ram
43k
Sorry, I see how harsh I come across. It's not good practice to use multiple versions of R in the same project. I can understand legacy pro…
Answer: MEGA Analysis Issue on High-Performance Computer
by
Mensur Dlakic
★ 27k
> I have ensured that I am using the latest version of MEGA and that other applications are not consuming excessive resources during the an…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
BioinfGuru
★ 1.7k
Some of us are still learning and fall foul to knowledge limitation fairly regularly. Luckily we have people to put us in our place.
Answer: Running blastp with BLAST+ 2.15.0 against custom database; need to identify hits
by
GenoMax
141k
> I know that I should be able to collect protein sequences from the blastp results into a file, but I do not know how to do this. You c…
Comment: how to find genes that are significantly expressed in brain cortex samples
by
rheab1230
▴ 140
I got the normalized gene count from gtex portal. they use inverse quantile normalization
Comment: what's the genomic location and name of gene responsible for orange and black pa
by
Matthias Zepper
4.5k
It is not entirely off, but evidently also not correct. Melanin biosynthesis is a multistep process, that indeed prominently involves the…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
Ram
43k
> so a single Rscript could utilise multiple environments and versions How is that sane, let alone "better"? Also, why use `snap` for curl…
Comment: how to find genes that are significantly expressed in brain cortex samples
by
Ram
43k
Normalized how?
Comment: Duplicate marking, read names, and the SRA
by
GenoMax
141k
With public data one has to work with what is there. If the information about position is absent then only thing that could be done is to l…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
BioinfGuru
★ 1.7k
Or better yet. To have an R package that allows access to conda environments via "conda list env" so that environments can be switched with…
Comment: what's the genomic location and name of gene responsible for orange and black pa
by
GenoMax
141k
If GPT is right then it says that: > The specific gene responsible for the orange and non-orange (black or > gray) fur colors in cats is t…
Comment: what's the genomic location and name of gene responsible for orange and black pa
by
Jean-Karim Heriche
27k
As far as I know the Orange locus hasn't been mapped to a gene. Maybe this paper will help in narrowing the search: https://www.ncbi.nlm.ni…
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