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130 results • Page
2 of 3
Sort: Views
Rank
Views
Votes
Replies
4
votes
4
replies
289
views
Does adding reads cause batch effects?
kallisto
RNAseq
updated 5 days ago by
ATpoint
72k • written 5 days ago by
bioinfo
▴ 80
0
votes
4
replies
275
views
Identification of genes involved in my pathway
KEGG
keggGet
5 days ago by
smanzano250800
• 0
2
votes
5
replies
266
views
Embryo transcriptome
database
transcriptome
SRA
updated 1 day ago by
ATpoint
72k • written 1 day ago by
firefox91
• 0
0
votes
1
reply
255
views
Comparing loci across catalogs
Stacks
reference
alignment
RADseq
adegenet
updated 4 days ago by
rycro_c
• 0 • written 13 months ago by
Austin
• 0
2
votes
4
replies
238
views
Filter VCF file for variant alleles
VCF
variants
bcftools
vcftools
updated 6 days ago by
Ram
39k • written 6 days ago by
miguellarrazlopezdenovales
• 0
0
votes
2
replies
234
views
featurecounts not working on mirbase annotation file
usegalaxy
miRNA-seq
1 day ago by
demoraesdiogo2017
▴ 90
0
votes
2
replies
225
views
BCR/TCR analysis using target capture sequencing data
capture
ngs
TCR
BCR
6 days ago by
J.F.Jiang
▴ 900
0
votes
3
replies
221
views
hardfilter error
bam
recall
4 days ago by
bestone
▴ 10
1
vote
2
replies
219
views
The famous WGS dataset, Ashkenazi Trio?
wgs
dataset
updated 4 days ago by
thadjudkins2
• 0 • written 4 days ago by
herh
• 0
1
vote
3
replies
219
views
To call variants can I use my aligned WGS data as a reference genome
VCF
samtools
reference
genome
updated 6 days ago by
GenoMax
129k • written 6 days ago by
mls
• 0
1
vote
3
replies
210
views
My kernel is killing the pairtools dedup script, how to prevent that?
ubuntu
hic
pairtools
aws
updated 5 days ago by
GenoMax
129k • written 5 days ago by
NikhilP
▴ 20
1
vote
2
replies
208
views
how to look for interactions between different chromosomes
SNP
interactions
Gene
HiC
5 days ago by
rheab1230
▴ 140
0
votes
3
replies
206
views
Dada2 in Qiime2: losing reads during merging
Qiime2
Chimer
Dada2
updated 6 days ago by
andres.firrincieli
3.4k • written 7 days ago by
kamanovae
▴ 80
1
vote
2
replies
206
views
Combination of ROC CURVE
roccurve
R
AUC
2 days ago by
Maria17
▴ 20
1
vote
2
replies
205
views
Converting RefSeq protein accession IDs into entreZ IDs
RNA-SEQ
6 days ago by
Pegasus
▴ 90
1
vote
4
replies
198
views
Is hg38 on the multiz 30-way alignment inaccurate?
maf
UCSC
PHAST
multiz
1 day ago by
Daniel
▴ 30
0
votes
3
replies
193
views
minimap's SAM file MAPQ value for the unique alignments
minimap
MAPQ
RNAseq
5 days ago by
Mohd
▴ 20
0
votes
4
replies
193
views
Difference between USCS exon coordinates and ensembl
exons
Ensembl
1 day ago by
amy__
▴ 50
1
vote
3
replies
189
views
How to get a comperative result of 2 bed files?
bam
cnv
bed
updated 5 days ago by
Pierre Lindenbaum
154k • written 6 days ago by
herh
• 0
2
votes
3
replies
184
views
Same GEO Accession, different SRR number, how to download this RNA-seq paired-end data?
sra-toolkit
fastq
RNA-seq
SRA
updated 8 hours ago by
GenoMax
129k • written 10 hours ago by
ev97
• 0
2
votes
2
replies
182
views
bioinformatic analysis protocol performed by CD Genomics
Genomics
analysis
CD
Protocol
updated 7 hours ago by
Ram
39k • written 5 days ago by
linnet.roque6
▴ 10
1
vote
2
replies
182
views
sorting BAM file
BAM
updated 6 days ago by
ATpoint
72k • written 7 days ago by
Mohammad Amin
• 0
0
votes
1
reply
181
views
Processing WES VCF for case control GWAS analysis
GWAS
PLINK
updated 4 days ago by
raphael.B
▴ 360 • written 4 days ago by
sonsunjirachote
• 0
0
votes
3
replies
179
views
DEGseq for multiple samples
DEGseq
DEG
updated 5 days ago by
Ram
39k • written 5 days ago by
ALOUSH ALI
• 0
0
votes
4
replies
178
views
Limma returned only positive logFC values
edgeR
differential-expression
deg
limma
6 hours ago by
melissachua90
▴ 40
0
votes
0
replies
178
views
Different alternatives for downloading GWAS summary statistics en masse
GWAS
6 days ago by
Vincent Laufer
★ 2.9k
0
votes
1
reply
174
views
Differential protein expression analysis
R
proteomic
statistics
updated 12 hours ago by
dsull
★ 4.2k • written 3 days ago by
Ribo
▴ 40
0
votes
2
replies
174
views
Ambient RNA expression correction
scRNAseq
SoupX
Seurat
updated 6 days ago by
rpolicastro
12k • written 6 days ago by
Pac314
▴ 10
0
votes
2
replies
172
views
Diff Bind Questions
DiffBind
CHiP-Seq
updated 4 hours ago by
Ram
39k • written 1 day ago by
B.N.
• 0
0
votes
0
replies
169
views
Visualization App for RNASeq Differential Expression and Enrichment Analysis
differential
visualization
RNASeq
analysis
expression
enrichment
4 days ago by
Mark
• 0
1
vote
3
replies
164
views
Obtain a --gene-trans-map file after rnaSPAdes
rnaSPAdes
Trinity
1 day ago by
UserA
• 0
0
votes
2
replies
163
views
readGenericHeader() error message Limma
rna
limma
microarray
genomics
normalization
5 days ago by
survive
• 0
0
votes
0
replies
162
views
NMDS plotting issue
NMDS
metagenomic
4 days ago by
arshad1292
▴ 90
0
votes
1
reply
161
views
Merge different vcf files
vcf
updated 4 days ago by
Ram
39k • written 5 days ago by
caique.manochio
• 0
0
votes
1
reply
157
views
Where to get the molecular subtype information of STAD sample in TCGA
TCGA
database
updated 2 days ago by
Hamid Ghaedi
2.9k • written 2 days ago by
younglin113
▴ 50
0
votes
0
replies
156
views
busco id description
OrthoDB
BUSCO
updated 4 days ago by
Ram
39k • written 4 days ago by
angelina
• 0
1
vote
0
replies
150
views
Bayesian network for biological data using bnlearn
bnlearn
RNA-seq
bayesian-network
updated 4 days ago by
Ram
39k • written 4 days ago by
priyankamehta.1811
▴ 10
1
vote
2
replies
150
views
hisat2 Error 137
hisat2
RNA-seq
1 day ago by
Forough
▴ 10
0
votes
0
replies
145
views
jellyfish options
kmer
jellyfish
4 days ago by
Tele
• 0
0
votes
1
reply
142
views
Pairwise Alignment
Pairwise-Alignment
updated 1 day ago by
Ram
39k • written 2 days ago by
Fatemeh
• 0
0
votes
0
replies
142
views
decoupleR & Transcription Factory Activity Inference: pvalue or padj?
pvalue
padj
decoupleR
3 days ago by
OST
▴ 10
1
vote
0
replies
141
views
Integrating mRNA and microRNA analysis results
mRNA
microRNA
5 days ago by
abba647
▴ 10
0
votes
1
reply
139
views
CHiP-Seq Questions
DiffBind
CHiP-Seq
updated 1 day ago by
jared.andrews07
★ 14k • written 1 day ago by
B.N.
• 0
0
votes
0
replies
138
views
IGV insertions
insertions
IGV
4 days ago by
christoph.schubart
• 0
0
votes
0
replies
134
views
How to keep ComplexHeatmap from reordering annotations
Dendrogram
HeatmapAnnotations
R
Heatmap
ComplexHeatmap
3 days ago by
Manuel
• 0
1
vote
1
reply
128
views
mitochondrial genome, SRA PacBio sequencing.
Mitochondrial
PacBio
SRA
Mitogenome
updated 6 days ago by
GenoMax
129k • written 6 days ago by
hashim.rana11
▴ 20
0
votes
0
replies
127
views
microsatellite, SSR, using Galaxy
Galaxy
SSR
using
microsatellite
3 days ago by
m.esmaeilpour
▴ 10
0
votes
1
reply
126
views
Information on sequin RNA spike in standards
Sequin
Spike-in
RNA-seq
updated 1 day ago by
Ram
39k • written 1 day ago by
akainth
▴ 10
0
votes
0
replies
122
views
How to extract the surrogate variables from DNA methlation Data
sva
array
limma
methylation
updated 4 days ago by
GenoMax
129k • written 4 days ago by
Dablax
• 0
0
votes
0
replies
120
views
cnetplot enrichment graph to cytoscape
clusterprofiler
cnetplot
enrichplot
4 days ago by
Omics data mining
▴ 220
130 results • Page
2 of 3
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Alternative approach to rarefying in 16S rRNA analysis
Answer: Gene prediction software
Comment: retaining only the clusters of interest
Comment: retaining only the clusters of interest
Calculating read abundances across MAGs (question)
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Recent Replies
Comment: calculate p value and associated z score for snp-gene pair
by
rheab1230
▴ 140
Thank you so much for the information.
Comment: Gviz Coverage Plots
by
Ram
39k
I understand that but stick to one place at least for a while and always link to other places you've posted (reasonable places, we don't ne…
Comment: Gviz Coverage Plots
by
Researcher
• 0
Sorry, I didn't know that posting it on another forum was rude but I really need help with this.
Comment: Correct way to remove Nextera adapters from ITS sequences
by
mattze731
▴ 10
Trimmomatic allows to enter custom adapter sequences, but I don't see how this would change the outcome. Similarly, trimmomatic also allows…
Comment: phage genome submission in ncbi genebank
by
acvill
▴ 290
When running prokka, did you call the `--compliant` parameter to enforce Genbank compliance? https://github.com/tseemann/prokka#ncbi-genban…
Comment: Correct way to remove Nextera adapters from ITS sequences
by
Trivas
★ 1.2k
Some of these programs have a minimum size threshold for a read to be retained. You could play around with that to keep all trimmed reads 5…
Comment: retaining only the clusters of interest
by
seidel
11k
Could it be that idents needs a character string instead of integers? Also, you have an extra comma in your call after c(0:16).
Comment: retaining only the clusters of interest
by
Ram
39k
`idents` is probably a factor so even though you've removed cells with those level values, the factor level still remains. Don't worry abou…
Comment: Contigs to chromosomes annotation
by
GenoMax
129k
I would still recommend using `minimap2` and aligning against reference. It should go pretty fast. You can either work with PAF (default) f…
Comment: Diff Bind Questions
by
Ram
39k
I've moved this to a comment as it does not directly answer OP's question.
Comment: Diff Bind Questions
by
Daniel
▴ 30
I'm very new myself and there's plenty of people who can answer your question better than I can, but here is a resource I found extremely h…
Comment: Contigs to chromosomes annotation
by
alexandru.bologa.marian
▴ 50
If the number of contigs was so small I would manually check each alignment and edit the header of each contig,inserting the corresponding …
Comment: Gviz Coverage Plots
by
Ram
39k
Do not post on multiple fora just because you want a fast response, it's plain rude. At least point to the other post so we know you're ask…
Comment: Limma returned only positive logFC values
by
melissachua90
▴ 40
No the library sizes across conditions should be relatively homogenous because it's from the same dataset. I clustered the samples into sub…
Comment: Limma returned only positive logFC values
by
LChart
2.6k
It shouldn't, unless there's a misspecification in design. Is it the case that the library sizes are very different between the conditions …
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