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1,000 results • Page
1 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
48
views
How to keep ComplexHeatmap from reordering annotations
Dendrogram
HeatmapAnnotations
R
Heatmap
ComplexHeatmap
7 hours ago by
Manuel
• 0
0
votes
0
replies
54
views
Differential protein expression analysis
R
proteomic
statistics
10 hours ago by
Ribo
▴ 40
0
votes
1
reply
122
views
(ERR): "index/Trinity.fa" does not exist or is not a Bowtie 2 index Exiting now ...
bowtie2
align_stats
trinity
updated 10 hours ago by
GenoMax
129k • written 11 hours ago by
eimanpharmacist
▴ 20
0
votes
3
replies
175
views
What are recommended parameters for the local protein alignment ?
protein
alignment
updated 2 hours ago by
Vincent Laufer
★ 2.9k • written 16 hours ago by
Alexander
▴ 70
0
votes
0
replies
71
views
microsatellite, SSR, using Galaxy
Galaxy
SSR
using
microsatellite
20 hours ago by
m.esmaeilpour
▴ 10
0
votes
0
replies
82
views
decoupleR & Transcription Factory Activity Inference: pvalue or padj?
pvalue
padj
decoupleR
1 day ago by
OST
▴ 10
2
votes
3
replies
232
views
Low mapping percentage
mapping
STAR
RNAseq
11 hours ago by
Sib
▴ 40
0
votes
0
replies
103
views
Visualization App for RNASeq Differential Expression and Enrichment Analysis
differential
visualization
RNASeq
analysis
expression
enrichment
1 day ago by
Mark
• 0
0
votes
0
replies
92
views
calculate p value and associated z score for snp-gene pair
snp
association
gene
pvalue
1 day ago by
rheab1230
▴ 140
0
votes
0
replies
95
views
busco id description
OrthoDB
BUSCO
updated 1 day ago by
Ram
39k • written 1 day ago by
hembrom.angelina
• 0
0
votes
5
replies
294
views
how to Construct a Newick tree file from five large fasta files
tree
Newick
alignment
updated 1 day ago by
Joe
21k • written 1 day ago by
gunala.nikhil
• 0
0
votes
0
replies
108
views
NMDS plotting issue
NMDS
metagenomic
1 day ago by
arshad1292
▴ 90
0
votes
1
reply
131
views
featurecounts not working on mirbase annotation file
usegalaxy
miRNA-seq
updated 1 day ago by
GenoMax
129k • written 1 day ago by
demoraesdiogo2017
▴ 90
0
votes
0
replies
95
views
IGV insertions
insertions
IGV
1 day ago by
christoph.schubart
• 0
1
vote
0
replies
102
views
Bayesian network for biological data using bnlearn
bnlearn
RNA-seq
bayesian-network
updated 1 day ago by
Ram
39k • written 1 day ago by
priyankamehta.1811
▴ 10
0
votes
0
replies
92
views
jellyfish options
kmer
jellyfish
1 day ago by
Tele
• 0
0
votes
3
replies
156
views
hardfilter error
bam
recall
1 day ago by
bestone
▴ 10
0
votes
0
replies
82
views
cnetplot enrichment graph to cytoscape
clusterprofiler
cnetplot
enrichplot
1 day ago by
Omics data mining
▴ 220
0
votes
0
replies
90
views
How to extract the surrogate variables from DNA methlation Data
sva
array
limma
methylation
updated 1 day ago by
GenoMax
129k • written 1 day ago by
Dablax
• 0
1
vote
1
reply
359
views
Reads with highest MAPQ values from SAM files are showing mismatches to reference sequence and IGV classified them as supplementary reads
minimap
Nanopore
IGV
updated 1 day ago by
GenoMax
129k • written 1 day ago by
Mohd
▴ 20
0
votes
0
replies
90
views
Stratified sample assignment for analysis
experimental-design
stratification
updated 1 day ago by
Ram
39k • written 1 day ago by
fr
▴ 200
0
votes
0
replies
81
views
Convert tree into bifurcation table
Tree
Newick
ASR
Mutation
1 day ago by
Alexandre
• 0
0
votes
1
reply
140
views
Processing WES VCF for case control GWAS analysis
GWAS
PLINK
updated 1 day ago by
raphael.B
▴ 360 • written 1 day ago by
sonsunjirachote
• 0
0
votes
4
replies
268
views
convert data frame with character column to data frame with integer column
r
1 day ago by
atemedorri137798
• 0
4
votes
6
replies
1.5k
views
Why weblogo of biopython doesn't work?
Biopython
Weblogo
updated 2 days ago by
minakshiboruahassam
• 0 • written 9 months ago by
Plus
▴ 20
1
vote
2
replies
192
views
The famous WGS dataset, Ashkenazi Trio?
wgs
dataset
updated 1 day ago by
thadjudkins2
• 0 • written 2 days ago by
herh
• 0
1
vote
0
replies
127
views
Integrating mRNA and microRNA analysis results
mRNA
microRNA
2 days ago by
abba647
▴ 10
4
votes
4
replies
259
views
Does adding reads cause batch effects?
kallisto
RNAseq
updated 2 days ago by
ATpoint
72k • written 2 days ago by
bioinfo
▴ 80
0
votes
1
reply
145
views
Merge different vcf files
vcf
updated 1 day ago by
Ram
39k • written 2 days ago by
caique.manochio
• 0
0
votes
4
replies
250
views
Identification of genes involved in my pathway
KEGG
keggGet
2 days ago by
smanzano250800
• 0
0
votes
8
replies
310
views
The inchworm process failed. Trinity running error.
inchworm
transcriptome
trinity
updated 1 day ago by
GenoMax
129k • written 2 days ago by
Marta
• 0
1
vote
1
reply
139
views
Combination of ROC CURVE
roccurve
R
AUC
updated 2 days ago by
seidel
11k • written 2 days ago by
Maria17
▴ 20
1
vote
0
replies
83
views
Considering gaps in calculating conservation score from MSA
multiple
alignment
sequence
conservation
python
2 days ago by
Jonathan Lefebre
▴ 50
0
votes
3
replies
167
views
DEGseq for multiple samples
DEGseq
DEG
updated 2 days ago by
Ram
39k • written 2 days ago by
ALOUSH ALI
• 0
0
votes
0
replies
74
views
Metabolomics Data Annotation
annotation
metabolomics
camera
updated 2 days ago by
Ram
39k • written 2 days ago by
Rishabh Jha
• 0
1
vote
3
replies
187
views
My kernel is killing the pairtools dedup script, how to prevent that?
ubuntu
hic
pairtools
aws
updated 2 days ago by
GenoMax
129k • written 3 days ago by
NikhilP
▴ 20
2
votes
2
replies
173
views
bioinformatic analysis protocol performed by CD Genomics
Genomics
CD
analysis
bioinformatic
Protocol
updated 2 days ago by
Dr William Klubinski
▴ 80 • written 3 days ago by
linnet.roque6
▴ 10
3
votes
12
replies
2.1k
views
What is NCBI Gene ID, where to find it and how to convert to entrez ID?
RNA-Seq
updated 2 days ago by
Pegasus
▴ 90 • written 3.7 years ago by
mnazir
▴ 10
0
votes
0
replies
102
views
RRBS fastq - biased per base sequence content
fastqc
rrbs
3 days ago by
mbk0asis
▴ 660
0
votes
0
replies
94
views
PRSice-2 using SNPs with extremely low P-value
PRSice-2
SNP
3 days ago by
Apprentice
▴ 140
0
votes
0
replies
299
views
What are the existing proposals for how to approach genomic coordinates in a pangenome reference environment?
coordinates
pangenome
genomic
3 days ago by
Vincent Laufer
★ 2.9k
0
votes
0
replies
102
views
Determining Cutoff for score in a bed file in ATAC-seq Data Analysis
bed
ATAC-seq
updated 3 days ago by
Ram
39k • written 3 days ago by
Mah
• 0
1
vote
3
replies
213
views
To call variants can I use my aligned WGS data as a reference genome
VCF
samtools
reference
genome
updated 3 days ago by
GenoMax
129k • written 3 days ago by
mls
• 0
0
votes
0
replies
105
views
snpEff error. No CDS checked
snpEff
gtf
WES
3 days ago by
fifty_fifty
▴ 40
0
votes
0
replies
104
views
Tool to align metagenomic data to reference genome
tool
metagenomics
alignment
3 days ago by
Maddie
• 0
1
vote
2
replies
189
views
how to look for interactions between different chromosomes
SNP
interactions
Gene
HiC
2 days ago by
rheab1230
▴ 140
2
votes
4
replies
228
views
Filter VCF file for variant alleles
VCF
variants
bcftools
vcftools
updated 3 days ago by
Ram
39k • written 3 days ago by
miguellarrazlopezdenovales
• 0
0
votes
0
replies
81
views
Pore-C-Snakemake output files
contacts
3 days ago by
oksana03fel
• 0
1
vote
0
replies
105
views
Linear models with limma: coefficients not estimatable, are the others OK?
limma
3 days ago by
fr
▴ 200
0
votes
2
replies
170
views
Ambient RNA expression correction
scRNAseq
SoupX
Seurat
updated 3 days ago by
rpolicastro
12k • written 3 days ago by
Pac314
▴ 10
1,000 results • Page
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Answer: [Meta] Use of AI
Discard Alignment With Mismatches From A Bam File
Comment: Help with running ATAC using Encode pipeline
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[Meta] Use of AI
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Answer: Filtering mitochondrial reads from ATAC-Seq aligned reads- what to do with reads
by
LChart
2.6k
A read with RNEXT assigned to MT does indicate a mate that has been aligned to the mitochondria. In general, there should not be any DNA mo…
Comment: What are recommended parameters for the local protein alignment ?
by
Vincent Laufer
★ 2.9k
did you see my updated post? once we get past that, id be willing to tackle this.
Comment: [Meta] Use of AI
by
Vincent Laufer
★ 2.9k
@genomax the funny thing is, I couldn't agree more with literally everything in your post. I sat there nodding my head for the duration of …
Comment: Is a human genome file with reference as NCBI37 the same as hg19?
by
a5864557
• 0
I know GRCh37 is synonymous (with minor differences) with hg19. However, I'm wondering if NCBI37 is synonymous with GRCh37 and hg19. Maybe …
Answer: Is a human genome file with reference as NCBI37 the same as hg19?
by
GenoMax
129k
If you go to the GRCh37 page at NCBI you will see that `hg19` is a synonym (mostly used by UCSC as I recall): https://www.ncbi.nlm.nih.gov/…
Comment: Help with running ATAC using Encode pipeline
by
Chris
▴ 100
So do we have redundant in this case when we specify the path to fastq.gz files in both input file and json file? json file is .json, how a…
Comment: Is a human genome file with reference as NCBI37 the same as hg19?
by
a5864557
• 0
Note: I've also asked this [here][1] [1]: https://bioinformatics.stackexchange.com/questions/21101/is-a-human-genome-file-with-referenc…
Answer: [Meta] Use of AI
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GenoMax
129k
As you indicate, AI in some form or other is here to stay and we can't avoid it in our lives and on biostars. Main issue I see is the vali…
Answer: RNASeq gene labeling and mRNA filter from bulkRNA data.
by
rfran010
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featureCounts can extract this information and output a column for you during counting, presuming you input a GTF file. `extraAttributes …
Comment: What are recommended parameters for the local protein alignment ?
by
Alexander
▴ 70
Trying to do so ))
Comment: Help with running ATAC using Encode pipeline
by
rfran010
▴ 110
The "Input files" section is details on how you can specify your fastqs in the JSON. (You specify all pipeline parameters in the JSON.) Ess…
Comment: What are recommended parameters for the local protein alignment ?
by
Vincent Laufer
★ 2.9k
does this mean you understand pident now and are moving forward?
Answer: Random dataset and DESeq2
by
Vincent Laufer
★ 2.9k
@e38da452 Not only is this not surprising, it is the basis for an entire class of statistical techniques referred to as permutation bas…
Comment: (ERR): "index/Trinity.fa" does not exist or is not a Bowtie 2 index Exiting now
by
GenoMax
129k
> This generated multiple Trinity.fa files in the index folder Did the process complete successfully?
Comment: Random dataset and DESeq2
by
LChart
2.6k
I don't think you've given enough detail about your approach (what's the data? are you correcting for covariates? how did you shuffle? how …
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