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117,109 results • Page
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16S analysis for specie of bacteria identification
identification
Species
16S
Kraken2
just now by
Christopher
▴ 10
0
votes
1
reply
48
views
PCA plot no distinct cluster. Only p < 0.05 indicates significant DEGs, while adj p < 0.05 does not.
RNA-seq
padj
p-value
updated just now by
swbarnes2
14k • written 4 hours ago by
May Ling
• 0
0
votes
0
replies
5
views
abundance_estimates_to_matrix.pl in Trinity is not generating any matrices / output
trinity
updated 5 minutes ago by
GenoMax
142k • written 10 minutes ago by
jway
• 0
0
votes
1
reply
19
views
What is a good way to do gene differentials in single cell data where one group is small 90 cells and the other group 30,000 cells or 2000 cells.
cell
RNA-Seq
single
updated 10 minutes ago by
GenoMax
142k • written 50 minutes ago by
shahzaibali
• 0
799
votes
167
replies
144k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 4 months ago by
Biostar
2.8k • written 7.5 years ago by
Istvan Albert
100k
0
votes
1
reply
50
views
Trying to understand warning from MACS2 about too few paired peaks and differing results in DiffBind
MACS2
ATACseq
DiffBind
updated 1 hour ago by
jared.andrews07
★ 17k • written 5 hours ago by
atan
• 0
0
votes
2
replies
84
views
What do the transcript variant # mean in RefSeq?
refseq
updated 1 hour ago by
Ram
44k • written 4 hours ago by
curious
▴ 750
4
votes
6
replies
225
views
Mouse or Rat Gene Expression Data Similar to GTEx
whole-body
expression
atlas
58 minutes ago by
Shicheng Guo
★ 9.4k
1
vote
2
replies
161
views
Error when looping over multiple columns in a data frame in R
Statistics
R
4 hours ago by
Mohamed Samir
▴ 30
2
votes
0
replies
72
views
Job:
Permanent Position as Researcher/Computational Biologist at the National Genomics Infrastructure (Sweden)
Genomics
Sequencing
Sweden
Stockholm
SciLifeLab
4 hours ago by
Matthias Zepper
4.6k
0
votes
1
reply
55
views
BEAST2.5 Chloroplast Divergence Time using Fossil Records
BEAST2.5
Fossil
updated 5 hours ago by
Ram
44k • written 5 hours ago by
a.bibek52
▴ 10
3
votes
7
replies
3.9k
views
Difference in Bismark output methylation call files and coverage files
RRBS
Bismark
DNA-methylation
updated 4 hours ago by
Papyrus
★ 2.9k • written 3.9 years ago by
linelr
▴ 40
0
votes
0
replies
62
views
Job:
2 PhD Students in single-cell bioinformatics
NGS
4 hours ago by
mtabaka
• 0
0
votes
1
reply
65
views
minfi::getQC - badsamplecutoff 10.5
getqc
minfi
methylation
EPICv2
updated 5 hours ago by
Papyrus
★ 2.9k • written 5 hours ago by
June
• 0
0
votes
2
replies
593
views
minfi::getQC - is default badsamplecutoff of 10.5 always appropriate? ~half of samples fail by this measure
getqc
ewas
minfi
updated 5 hours ago by
June
• 0 • written 10 months ago by
rkb965
• 0
2
votes
5
replies
210
views
Z score
Z-score
updated 5 hours ago by
Ram
44k • written 12 hours ago by
Akash D
▴ 60
1
vote
5
replies
189
views
Error with BiocParallel. No barcodes files found
Barcodes
scRNA-seq
SingleCellExperiment
updated 5 hours ago by
Pierre Lindenbaum
162k • written 9 hours ago by
NTerway
• 0
1
vote
2
replies
121
views
Unexpected read length from NGS
NGS
Illumina
updated 8 hours ago by
ATpoint
82k • written 10 hours ago by
QX
• 0
0
votes
0
replies
48
views
Tools for chromosomal aneuploidy detection
genetics
aneuploidy
NGS
human
8 hours ago by
adarsh_pp
▴ 40
1
vote
6
replies
265
views
samtools write-index
samtools
updated 9 hours ago by
aw7
▴ 310 • written 1 day ago by
LucisTheFather
• 0
0
votes
2
replies
188
views
How do we do quantification using stringtie merge option for all the merged samples generated.
stringtie
quantification
updated 10 hours ago by
i.sudbery
19k • written 1 day ago by
Varsha
• 0
1
vote
2
replies
119
views
How to interpret this plotMDS of three disease clusters?
microarray
plotMDS
DEGs
updated 8 hours ago by
ATpoint
82k • written 11 hours ago by
egascon
• 0
0
votes
0
replies
48
views
GWAS or QTL mapping in RIL population
GWAS
RIL
10 hours ago by
韩雨
• 0
0
votes
0
replies
57
views
VEP annotation tool: "." isn't numeric in addition (+)
VEP
VCF
updated 5 hours ago by
Ram
44k • written 10 hours ago by
emmanouil.a
▴ 120
11
votes
13
replies
6.6k
views
7 follow
log2 fold change in RNA-seq analysis
fold
log2
change
updated 5 hours ago by
May Ling
• 0 • written 2.4 years ago by
wmsalsah
▴ 10
0
votes
1
reply
232
views
GWAS Phenotypes
GWAS
updated 11 hours ago by
韩雨
• 0 • written 5 weeks ago by
solomoncharles77
▴ 90
5
votes
4
replies
5.1k
views
6 follow
Classic threshold for log2 fold change in RNA-seq experiment
RNA-Seq
updated 11 hours ago by
May Ling
• 0 • written 3.9 years ago by
Mozart
▴ 330
0
votes
1
reply
88
views
Cellranger-multi : Demultiplexing and Analyzing 5’ Immune Profiling Libraries Pooled with Hashtags
5InmuneProfiling
nf-core
scRNAseq
cellranger-multi
Nextflow
updated 8 hours ago by
GenoMax
142k • written 11 hours ago by
azeu
• 0
0
votes
0
replies
41
views
Assigning Micro-C read pairs to nucleosomes called from MNase-seq data?
Hi-C
MNase-Seq
12 hours ago by
Linus
• 0
7
votes
3
replies
13k
views
Z score in RNAseq
RNA-Seq
Zscore
updated 12 hours ago by
Akash D
▴ 60 • written 6.5 years ago by
rob.costa1234
▴ 310
0
votes
1
reply
109
views
Free AI for R programming
R
updated 5 hours ago by
Ram
44k • written 12 hours ago by
mohamadzare6022
▴ 10
7
votes
13
replies
779
views
7 follow
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 6 hours ago by
i.sudbery
19k • written 4 weeks ago by
Estevão
▴ 10
0
votes
0
replies
74
views
Extracting haplotype-specific annotations from splicing graph
vg
16 hours ago by
Juhyun
• 0
0
votes
0
replies
66
views
miloR - object 'as.SimpleList' of mode 'function' was not found when running calcNhoodDistance
scRNA-seq
seurat
miloR
16 hours ago by
shuaizh117
▴ 10
0
votes
0
replies
72
views
Phyloseq returning black bars for plot_bar
phyloseq
bioconductor
R
20 hours ago by
Jacob
• 0
1
vote
8
replies
843
views
Random Access remote BAM files
htslib
BAM
updated 22 hours ago by
a.penatauber
• 0 • written 3 months ago by
Lucas R.F.
▴ 10
0
votes
0
replies
77
views
Cancer vs Normal Cell Classification Based on SNVs
cancer
23 hours ago by
dglad
• 0
0
votes
4
replies
191
views
merge overlaps and remove non overlap genomic windows
BED
intersection
overlap
23 hours ago by
reza
▴ 300
0
votes
1
reply
104
views
Flag multiple filtering steps on VCF files using VEP
VEP
VCF
updated 5 hours ago by
Ram
44k • written 1 day ago by
avelarbio46
▴ 30
0
votes
1
reply
119
views
Small secondary peak for per sequence GC content - FASTQC results (bulk RNA-seq)
RNAseq
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Fossil
• 0
1
vote
1
reply
161
views
Construction of circos plot from WGS data
WGS
Circos
updated 1 day ago by
Ram
44k • written 1 day ago by
Anitha
▴ 10
1
vote
3
replies
210
views
Trimmomatic running but files containing purged reads are empty
fastqc
fastq
trimmomatic
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Wilber0x
▴ 50
0
votes
0
replies
83
views
How to find nucleotide changes and the predicted effect when comparing two genomes
BLAST
alignment
updated 1 day ago by
Ram
44k • written 1 day ago by
Melissa
• 0
5
votes
3
replies
178
views
FastQC interpretation - 16S sequencing
interpretation
amplicon
Fastqc
16S
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Christopher
▴ 10
0
votes
0
replies
91
views
Subset of ATAC-seq peaks has high variance
atac-seq
edgeR
R
normalization
14 hours ago by
Tim
• 0
2
votes
6
replies
270
views
How to get the ratio of allele counts from GATK derived VCF file?
Freebayes
GATK
SNP
VCF
13 hours ago by
anikcropscience
▴ 230
0
votes
0
replies
92
views
KEGG pathway enrichment analysis in Zea mays with R
KEGG
Zea-mays
R
updated 1 day ago by
Ram
44k • written 1 day ago by
letizia.ottaviani
• 0
0
votes
6
replies
256
views
from CRAM to fastq
FASTQ
WGS
CRAM
updated 23 hours ago by
ATpoint
82k • written 1 day ago by
machaalani29
• 0
0
votes
0
replies
94
views
News:
Bioinformatic Analysis of Transposable Elements course
Genome-Annotation
TE
Manual-Curation
Transposable-Elements
updated 1 day ago by
Ram
44k • written 1 day ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
121
views
No output when converting transcript IDs to gene symbols
RNA-seq
updated 1 day ago by
Ram
44k • written 1 day ago by
ashkan
▴ 160
117,109 results • Page
1 of 2343
Recent Votes
A: VCF files: Change Chromosome Notation
Comment: Z score
Comment: Mouse or Rat Gene Expression Data Similar to GTEx
Answer: Mouse or Rat Gene Expression Data Similar to GTEx
Answer: Mouse or Rat Gene Expression Data Similar to GTEx
Answer: Mouse or Rat Gene Expression Data Similar to GTEx
A: VCF files: Change Chromosome Notation
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142k
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bioinfo
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Answer: PCA plot no distinct cluster. Only p < 0.05 indicates significant DEGs, while ad
by
swbarnes2
14k
Never use uncorrected p-values with RNASeq. Your PCA is suggesting that your sample groups are not very different, and the DEG tests con…
Comment: What is a good way to do gene differentials in single cell data where one group
by
ATpoint
82k
I would keep it transparent. Do DE by subsetting large to small group. Do that randomly many times, then either average stats or use some s…
Answer: Trying to understand warning from MACS2 about too few paired peaks and differing
by
jared.andrews07
★ 17k
Without looking at the actual sequence for each genome, my guess is that the Echinobase reference just matches much more closely to the org…
Comment: What do the transcript variant # mean in RefSeq?
by
Ram
44k
> It does not seem to be the longest transcript. Is it the canonical transcript? Longest == canonical. If you're looking for the transcrip…
Comment: Mouse or Rat Gene Expression Data Similar to GTEx
by
Shicheng Guo
★ 9.4k
Hi ATpoint, Thank you for your responses. My apologies if my inquiries have seemed one-sided. I greatly value the collaborative spirit of t…
Comment: Mouse or Rat Gene Expression Data Similar to GTEx
by
ATpoint
82k
Team? A team helps each other out. You only take help by posting your regular lazy do-my-work questions and never give anything back. Save …
Comment: What do the transcript variant # mean in RefSeq?
by
GenoMax
142k
> What do these correspond to? It does not seem to be the longest transcript. Is it the canonical transcript? Those are just different tra…
Answer: Mouse or Rat Gene Expression Data Similar to GTEx
by
jared.andrews07
★ 17k
MGI has a [Gene Expression Database](https://www.informatics.jax.org/expression.shtml) that'll largely get you what you want.
Comment: Difference in Bismark output methylation call files and coverage files
by
Papyrus
★ 2.9k
Your files end in `CpG_report` so they are the "genome-wide cytosine report output". If you look at the [Bismark documentation][1] you will…
Comment: Error when looping over multiple columns in a data frame in R
by
Mohamed Samir
▴ 30
Dear Jeremy, Thanks. What I could not understand why you wrote it like : cutpoint_results[[col_name]] ? Is it because it is a list result…
Comment: BEAST2.5 Chloroplast Divergence Time using Fossil Records
by
Ram
44k
Do not use all caps - it's bad etiquette. I've fixed things for you this time.
Comment: minfi::getQC - badsamplecutoff 10.5
by
Papyrus
★ 2.9k
I've recently also analyzed EPICv2 and have noticed that the log2 median intensities (and particularly the "uMed" channel), for an otherwis…
Comment: log2 fold change in RNA-seq analysis
by
May Ling
• 0
Thank you so much for the confirmation Sir! Appreciate that. I think the paragraph was trying to say that: a fold change greater than **…
Comment: Difference in Bismark output methylation call files and coverage files
by
skdv2522
• 0
Chr1 192 + 0 0 CG CGA Chr1 193 - 0 0 CG CGA Chr1 197 + 0 0 CG CGT Chr1 198 - 0 0 CG CGG Chr1 218 + 0 0 CG CGA Chr1 …
Comment: Error with BiocParallel. No barcodes files found
by
Pierre Lindenbaum
162k
cross-posted: https://stackoverflow.com/questions/78522566/ > Do not post on multiple forums - that is just bad etiquette. What's worse, y…
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