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173 results • Page
3 of 4
Sort: Views
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Views
Votes
Replies
0
votes
1
reply
183
views
How to find overlap of clusters in two seurat porject
clustering
seurat
updated 1 day ago by
Adam
▴ 30 • written 2 days ago by
J
• 0
1
vote
0
replies
183
views
News:
Landscape Genomics course in Switzerland
LFMM
Landscape-Genomics
Sambada
R
Local-Adaptation
12 hours ago by
carlopecoraro2
★ 2.5k
2
votes
2
replies
182
views
MA plot of shrunken fold change
MA-plot
Deseq2
updated 2 days ago by
ATpoint
82k • written 2 days ago by
Sudip
• 0
0
votes
0
replies
175
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 6 days ago by
Ram
43k • written 6 days ago by
SineWave
• 0
0
votes
1
reply
175
views
Differential Accessibility
DiffBind
updated 3 days ago by
Ram
43k • written 3 days ago by
Shloka
• 0
0
votes
1
reply
175
views
Deseq2
Deseq2
updated 2 days ago by
Jack Tierney
▴ 360 • written 2 days ago by
Sudip
• 0
0
votes
1
reply
175
views
Subsetting and merging back Seurat Object brings different results
Seurat
9 hours ago by
Bine
▴ 60
0
votes
0
replies
171
views
RNA-seq: full length gene
RNA-seq
updated 6 days ago by
Ram
43k • written 6 days ago by
Nargis
• 0
0
votes
1
reply
168
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
updated 1 day ago by
Adam
▴ 30 • written 2 days ago by
Ahiad Chen Zion
• 0
0
votes
1
reply
167
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK
recalibration
updated 21 hours ago by
GenoMax
142k • written 1 day ago by
mgranada3
▴ 30
0
votes
1
reply
165
views
Downloading full alignments from Pfam
pfam
updated 4 days ago by
GenoMax
142k • written 4 days ago by
bef1
• 0
1
vote
1
reply
161
views
Including plasmid in alignment
Bacteria
Transcriptomics
BOWTIE2
STAR
2 days ago by
heelpPlease
• 0
0
votes
1
reply
160
views
metagenomic virome quality assessment
viromics
metagenomics
updated 3 days ago by
Ram
43k • written 3 days ago by
Petchimuthu
• 0
0
votes
1
reply
157
views
unable to get feature count results
featureCounts
updated 2 days ago by
Ram
43k • written 2 days ago by
Ravita
• 0
1
vote
0
replies
156
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
6 days ago by
KABILAN
▴ 70
0
votes
1
reply
154
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 1 day ago by
i.sudbery
19k • written 1 day ago by
Edmond
• 0
0
votes
0
replies
153
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
6 days ago by
turcoa1
• 0
0
votes
0
replies
152
views
News:
Goodbye, Slow Code? How BioNumpy can Redefine Python’s Role in Bioinformatics!
BioNumPy
Python
NumPy
updated 2 days ago by
Ram
43k • written 2 days ago by
Chakri
• 0
0
votes
2
replies
148
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
3 days ago by
Lluís R.
★ 1.2k
1
vote
2
replies
147
views
Odd alignment question/finding
Alignment
updated 14 hours ago by
ATpoint
82k • written 20 hours ago by
poordumbsillyidiot
• 0
0
votes
0
replies
139
views
Filter low express genes in microarray data
microarray
5 days ago by
Chris
▴ 260
0
votes
1
reply
139
views
How to solve DESeq2 Error in checkFullRank(modelMatrix)?
RNA-Seq
DESeq2
updated 3 days ago by
i.sudbery
19k • written 3 days ago by
DOBI
• 0
0
votes
0
replies
136
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
5 days ago by
tnminh89
▴ 10
0
votes
4
replies
133
views
What purposes can TPM values be used for?
RNA-seq
TPM
Normalization
DESeq2
updated 7 hours ago by
jared.andrews07
★ 16k • written 8 hours ago by
JH
• 0
0
votes
1
reply
130
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Ruqaiya
• 0
0
votes
1
reply
128
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Winter
• 0
2
votes
4
replies
127
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
1 hour ago by
Qroid
▴ 40
4
votes
0
replies
128
views
Herald:
The Biostar Herald for Monday, April 29, 2024
herald
3 days ago by
Biostar
2.7k
0
votes
0
replies
123
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
2 days ago by
Jacob
• 0
0
votes
0
replies
123
views
Seurat object reductions (PCA, UMAP,..) after subsetting data
Seurat
2 days ago by
Bine
▴ 60
0
votes
0
replies
123
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
2 days ago by
8armed
• 0
0
votes
0
replies
121
views
barcode of TCR-sequencing
barcode
2 days ago by
yueli7
▴ 250
0
votes
0
replies
120
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics
metacyc
enzyme
pathway
genomics
1 day ago by
O.rka
▴ 710
0
votes
0
replies
120
views
News:
Online course: Meta-analysis in R - last 2 seats left
Meta-Analysis
Statistics
R
updated 2 days ago by
Ram
43k • written 2 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
120
views
Synteny analysis
bacterial
synteny
genome
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Namil
• 0
0
votes
0
replies
120
views
adjusting for confounders in LMER in R
confounders
LMER
R
updated 3 days ago by
dariober
14k • written 4 days ago by
rene.j.erhardt
▴ 20
0
votes
0
replies
120
views
Using limma in methylation EM-seq?
EM-seq
methylation
3 days ago by
Lluís R.
★ 1.2k
0
votes
0
replies
116
views
Somatic variant calling with Mutect2 using 2 matched-normals for one sample
cancer
mutect
variant-calling
GATK
somatic-variants
updated 2 days ago by
Ram
43k • written 2 days ago by
Alexandros
• 0
0
votes
1
reply
114
views
Mutect2 for mitochondria variant discovery
mutect2
mitochondria
updated 1 day ago by
Ram
43k • written 1 day ago by
ernestine.kubi
• 0
0
votes
0
replies
110
views
human gut metagenome taxonomy profile table and KO profile table from big cohort
metagenome
gut
human
2 days ago by
fanglujing
▴ 60
1
vote
3
replies
107
views
DiffBind: no peaks in DBA
MACS2
DiffBind
ChIP-seq
updated 2 hours ago by
jared.andrews07
★ 16k • written 6 hours ago by
yvonneh
▴ 10
0
votes
0
replies
108
views
News:
Online course: Genome Annotation
Genome-Assembly
Genome-Annotation
3 days ago by
carlopecoraro2
★ 2.5k
0
votes
2
replies
107
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
5 hours ago by
Chen
• 0
0
votes
0
replies
106
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
2 days ago by
Adyasha
• 0
1
vote
1
reply
101
views
Super ehancers
enhancers
updated 7 hours ago by
jared.andrews07
★ 16k • written 12 hours ago by
Oburah
• 0
1
vote
1
reply
98
views
What analysis suitable to identify similarly expressed genes between two samples (treated vs untreated). Contrary to DGE analysis,
Gene-Expression
RNA
NOISeq
DGE
updated 6 hours ago by
Ram
43k • written 10 hours ago by
alifafiq1
• 0
0
votes
0
replies
99
views
LEfSe
LEfSe
3 days ago by
benkosta
• 0
1
vote
1
reply
98
views
Discrepancy in read counts from fastq
downsampling
fastq
updated 6 hours ago by
Ram
43k • written 13 hours ago by
marco.barr
▴ 90
0
votes
0
replies
96
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass
Bioinformatics
spectrometry
Proteins
3 days ago by
atharvakarkare14
▴ 30
0
votes
1
reply
95
views
How to perform single cell multimodal integration using Seurat for Geo datasets
multimodal-analysis
single-cell
updated 4 hours ago by
Ram
43k • written 16 hours ago by
nithya
• 0
173 results • Page
3 of 4
Recent Votes
Answer: Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
How to convert plink data from 38th assembly to 37
How to convert plink data from 38th assembly to 37
Comment: How to access TCGA samples that were treated with a specific drug?
Comment: Normalize scRNAseq data to housekeeping genes to compare several datasets
Comment: Converting CRAM to FastQ
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Recent Replies
Comment: Does comparing two different groups to a common third group introduce bias in th
by
Qroid
▴ 40
Are you thinking about a specific scenario? If so, can you provide more info? I think the basic answer is that, yes, your choice of group C…
Answer: Bedtools merge minimum overlap?
by
harold.smith.tarheel
★ 4.9k
Bedtools [intersect][1] allows you to specify the fraction of overlap between two BED (or BAM) files using the F/f/r flags. You could split…
Comment: How to access TCGA samples that were treated with a specific drug?
by
Qroid
▴ 40
Sorry, I should have been more specific. By "that list" I mean what's populated in the Therapeutic Agents tab when no filters are applied. …
Comment: Bedtools merge minimum overlap?
by
bk11
★ 2.4k
Not sure if you wanting to do like this- cat your_input.bed chr1 100 200 region1 + chr1 180 300 regi…
Comment: Extract gRNA sequence using cutadapt
by
GenoMax
142k
If you know what the boundaries of your construct look like then trim the left-end of the read using the tag on that end (`ktrim=l`). Then …
Comment: Extract gRNA sequence using cutadapt
by
gernophil
▴ 80
> Not every read in your data is going to match a guide. That is also true for sure. Let me clarify what I mean. For every read you should…
Answer: VG : No reference-sense paths available in the graph; falling back to generic pa
by
anovak
▴ 120
If your GFA has paths in it that are P lines with names that don't include a sample name, contig name, and separators, then those are what …
Comment: Extract gRNA sequence using cutadapt
by
GenoMax
142k
> if you look at a fastq file you should be able to tell for every read definitely, if it has a perfect match for a guide in it and what gu…
Answer: DiffBind: no peaks in DBA
by
jared.andrews07
★ 16k
Because `dba.analyze` is not meant to be run directly on a peaks file. Have you read the documentation? In addition, a ChIP-seq experiment…
Comment: Converting CRAM to FastQ
by
Maverick
▴ 10
Thank you so much! Will look it up right away.
Comment: Extract gRNA sequence using cutadapt
by
gernophil
▴ 80
> I don't think every guide is supposed to show up in these experiments as far as I have seen. You will get some guides with 0 counts as yo…
Comment: Converting CRAM to FastQ
by
GenoMax
142k
Use `samtools view ` for this conversion. See discussion in https://www.biostars.org/p/9592860/ Specifically @jkbonfield's comment here --…
Comment: How to access TCGA samples that were treated with a specific drug?
by
GenoMax
142k
No that was only from Breast cancer. You could try selecting all data and see if you are able to see all treatments in the set. No idea a…
Comment: Extract gRNA sequence using cutadapt
by
GenoMax
142k
I don't think every guide is supposed to show up in these experiments as far as I have seen. You will get some guides with 0 counts as you …
Comment: Extract gRNA sequence using cutadapt
by
gernophil
▴ 80
> Can you try lowering the k to k=9? Wouldn't that mess with the results since all my kmers are 20bp? > You don't have any duplicate sequ…
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