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117,126 results • Page
2 of 2343
Sort: Rank
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Votes
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5
votes
4
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5.2k
views
6 follow
Classic threshold for log2 fold change in RNA-seq experiment
RNA-Seq
updated 1 day ago by
May Ling
• 0 • written 3.9 years ago by
Mozart
▴ 330
1
vote
1
reply
124
views
Cellranger-multi : Demultiplexing and Analyzing 5’ Immune Profiling Libraries Pooled with Hashtags
5InmuneProfiling
nf-core
scRNAseq
cellranger-multi
Nextflow
updated 1 day ago by
GenoMax
142k • written 1 day ago by
azeu
▴ 10
0
votes
0
replies
59
views
Assigning Micro-C read pairs to nucleosomes called from MNase-seq data?
Hi-C
MNase-Seq
1 day ago by
Linus
• 0
7
votes
3
replies
13k
views
Z score in RNAseq
RNA-Seq
Zscore
updated 1 day ago by
Akash D
▴ 60 • written 6.5 years ago by
rob.costa1234
▴ 310
0
votes
1
reply
141
views
Free AI for R programming
R
updated 1 day ago by
Ram
44k • written 1 day ago by
mohamadzare6022
▴ 10
7
votes
13
replies
813
views
7 follow
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 1 day ago by
i.sudbery
19k • written 4 weeks ago by
Estevão
▴ 10
0
votes
0
replies
94
views
Extracting haplotype-specific annotations from splicing graph
vg
1 day ago by
Juhyun
• 0
0
votes
0
replies
89
views
miloR - object 'as.SimpleList' of mode 'function' was not found when running calcNhoodDistance
scRNA-seq
seurat
miloR
1 day ago by
shuaizh117
▴ 10
0
votes
0
replies
89
views
Phyloseq returning black bars for plot_bar
phyloseq
bioconductor
R
1 day ago by
Jacob
• 0
3
votes
8
replies
871
views
Random Access remote BAM files
htslib
BAM
updated 1 day ago by
a.penatauber
• 0 • written 3 months ago by
Lucas R.F.
▴ 20
0
votes
0
replies
94
views
Cancer vs Normal Cell Classification Based on SNVs
cancer
1 day ago by
dglad
• 0
0
votes
4
replies
210
views
merge overlaps and remove non overlap genomic windows
BED
intersection
overlap
1 day ago by
reza
▴ 300
0
votes
1
reply
124
views
Flag multiple filtering steps on VCF files using VEP
VEP
VCF
updated 1 day ago by
Ram
44k • written 1 day ago by
avelarbio46
▴ 30
0
votes
1
reply
138
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
2
replies
226
views
Construction of circos plot from WGS data
WGS
Circos
13 hours ago by
Anitha
▴ 10
1
vote
3
replies
229
views
Trimmomatic running but files containing purged reads are empty
fastqc
fastq
trimmomatic
updated 2 days ago by
GenoMax
142k • written 2 days ago by
Wilber0x
▴ 50
0
votes
0
replies
100
views
How to find nucleotide changes and the predicted effect when comparing two genomes
BLAST
alignment
updated 1 day ago by
Ram
44k • written 2 days ago by
Melissa
• 0
5
votes
3
replies
197
views
FastQC interpretation - 16S sequencing
interpretation
amplicon
Fastqc
16S
updated 2 days ago by
GenoMax
142k • written 2 days ago by
Christopher
▴ 10
0
votes
0
replies
109
views
Subset of ATAC-seq peaks has high variance
atac-seq
edgeR
R
normalization
1 day ago by
Tim
• 0
2
votes
6
replies
289
views
How to get the ratio of allele counts from GATK derived VCF file?
Freebayes
GATK
SNP
VCF
1 day ago by
anikcropscience
▴ 230
0
votes
0
replies
101
views
KEGG pathway enrichment analysis in Zea mays with R
KEGG
Zea-mays
R
updated 1 day ago by
Ram
44k • written 2 days ago by
letizia.ottaviani
• 0
0
votes
6
replies
269
views
from CRAM to fastq
FASTQ
WGS
CRAM
updated 1 day ago by
ATpoint
82k • written 2 days ago by
machaalani29
• 0
0
votes
0
replies
99
views
News:
Bioinformatic Analysis of Transposable Elements course
Genome-Annotation
TE
Manual-Curation
Transposable-Elements
updated 1 day ago by
Ram
44k • written 2 days ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
125
views
No output when converting transcript IDs to gene symbols
RNA-seq
updated 1 day ago by
Ram
44k • written 2 days ago by
ashkan
▴ 160
3
votes
1
reply
156
views
vg autoindex seems stuck after a week of running
vg
pangenome
updated 2 days ago by
Jouni Sirén
▴ 380 • written 2 days ago by
StevieP
▴ 10
0
votes
0
replies
107
views
MAFFT alignment report
RNA
Alignment
MAFFT
Linux
updated 1 day ago by
Ram
44k • written 2 days ago by
Ghada
• 0
0
votes
3
replies
291
views
Kraken2 Custom Database non-deterministic results
Metagenomics
kraken2
updated 2 days ago by
colindaven
6.4k • written 3 days ago by
Bjorn
• 0
0
votes
1
reply
147
views
How to get 2 seurat objects into a DEseq
Seurat
DEseq
updated 1 day ago by
Ram
44k • written 2 days ago by
He11oJe11o
• 0
0
votes
0
replies
88
views
Rescaling normalized enrichment score (NES)
heatmap
2 days ago by
CTLong
▴ 110
0
votes
3
replies
205
views
Splitting query fasta file for Diamond Blastp make the process faster?
DIAMOND
10 hours ago by
kmat
• 0
0
votes
1
reply
147
views
Mapping difference with BWA
variant-calling
samtools
bam
BWA
genomics
updated 2 days ago by
ATpoint
82k • written 2 days ago by
rj.rezwan
• 0
0
votes
0
replies
102
views
Kegg Pathways to Circos
Genomics
KEGG
Circos
2 days ago by
dlera.lozano
▴ 10
0
votes
0
replies
113
views
DIFFBIND boxplot results, p value not significant
DiffBind
ChIP-seq
2 days ago by
RD
▴ 10
3
votes
6
replies
333
views
Problem in getting geo file through GEOQUERY
geoquery
Geo
updated 1 day ago by
Ram
44k • written 2 days ago by
anasjamshed
▴ 120
0
votes
1
reply
179
views
Multi-ploid data in ANGSD and NGSadmix
ancestry
diploid
haploid
admixture
updated 2 days ago by
andersdetermig
▴ 20 • written 3 days ago by
Christopher
• 0
0
votes
2
replies
346
views
transanno liftvcf "Error: length of chromosome [chr] is not equal to length in chain file. Are you using correct reference?"
liftover
transanno
2 days ago by
ezz3
• 0
1
vote
10
replies
624
views
Add stats to the plot
R
2 days ago by
Ghada
• 0
0
votes
4
replies
233
views
Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
GATK
UnifiedGenotyper
2 days ago by
shpak.max
▴ 50
2
votes
4
replies
260
views
Allele count of 2 for homoplasmic MT variants in VCF
Variant-Calling
GATK
VCF
1 day ago by
Arton
▴ 10
1
vote
3
replies
197
views
downloading chemical database from ChEMBL
ChEMBL
PyRMD
Virtual-Screening
updated 2 days ago by
GenoMax
142k • written 2 days ago by
s
• 0
0
votes
3
replies
184
views
Where are the illumina adapters on Trimmomatic take from?
rna-seq
trimmomatic
updated 2 days ago by
GenoMax
142k • written 2 days ago by
bioinfo
▴ 150
3
votes
2
replies
179
views
Multiplexing for pooled CRISPR screen sequencing
multiplex
CRISPR-screen
Illumina
2 days ago by
Tuấn Anh
• 0
2
votes
4
replies
1.2k
views
Is it possible to run CibersortX with a very small number of samples?
cibersortx
1 day ago by
Aspire
▴ 330
1
vote
3
replies
300
views
Functional enrichment analysis for unique gene IDs
RNA-SEQ
2 days ago by
Pegasus
▴ 100
0
votes
2
replies
198
views
Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis of Spleen Samples from Different Conditions
Seurat
scRNA-Seq
Single-Cell
3 days ago by
Shukai
• 0
1
vote
3
replies
199
views
Question about samtools view flags (paired reads vs. properly paired reads)
samtools
updated 2 days ago by
Pierre Lindenbaum
162k • written 3 days ago by
mrk
• 0
0
votes
3
replies
243
views
z-score of gene set
z-score
scRNA
gene-set
2 days ago by
Hien
• 0
3
votes
2
replies
206
views
converting transcript IDs (Ensembl) to gene symbols in R
RNA-seq
updated 2 days ago by
GenoMax
142k • written 3 days ago by
ashkan
▴ 160
0
votes
0
replies
107
views
Linking AMR Genes to Taxonomy in Soil Metagenomics
metagenomics
bacteria
wgs
AMR
resistome
updated 3 days ago by
GenoMax
142k • written 3 days ago by
LuciaNhu
• 0
1
vote
2
replies
183
views
How can we convert a vcf to fasta, so that I can blast some genes against that whole genome sequences?
blast
fasta
vcf
gene
updated 3 days ago by
Ram
44k • written 3 days ago by
Harshita
• 0
117,126 results • Page
2 of 2343
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Answer: Why some SNP's allele frequencies in gnomAD are so different between v2 and v4?
Comment: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
Why some SNP's allele frequencies in gnomAD are so different between v2 and v4?
Comment: Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLI
Comment: Single cell analysis: Unable to subset cells in seurat object using desired nFea
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Recent Replies
Comment: Harmony integration group.by.var parameter
by
jared.andrews07
★ 17k
>I am not sure, but using "Sample_ID" might remove the differences between the conditions right ? More than likely, it'd at least impact t…
Comment: Harmony integration group.by.var parameter
by
Picasa
▴ 640
Thanks jared.andrews07 for your answer. So, you are suggesting to use only "Donor" in the integration? ```r RunHarmony(seu_obj, group.by.…
Comment: Single cell analysis: Unable to subset cells in seurat object using desired nFea
by
sc_analysis
• 0
I am not sure what should be the cut off. Looking at the vlnplot before subsetting i thought most of the cells are falling under 7500 nfeat…
Comment: How to calculate cell type frequency between two groups in single cell data
by
Sara
▴ 30
Thank you for your comment and sorry if this question might be so basic. How can I normalize the number of cells? If I am not wrong the i…
Comment: Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files
by
Deepthi
• 0
I unzipped the fastq files to check whether reads are trimmed adapter or not. I have checked the quality control using fastqc they are go…
Comment: Mutation counts corrected by number of samples
by
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44k
> I want to compare the number of mutations This comparison will give you literally no useful information.
Answer: How to scrape BioMart data from https://sorfs.ugent.be/ website
by
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162k
something like: seq 1 100 4377380 | while read F ; do wget --no-check-certificate -O - "https://sorfs.ugent.be/database/micrope…
Answer: Harmony integration group.by.var parameter
by
jared.andrews07
★ 17k
The variability explained by the variables provided to `group.by.vars` is what Harmony will try to remove. Assuming you want to remove the …
Answer: Why some SNP's allele frequencies in gnomAD are so different between v2 and v4?
by
Jeremy Leipzig
22k
That SNP is in an HLA gene which has had a lot of attention and improvement over the years, ranging from kits to software to the reference …
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5.3k
What is the need of PBMC in your analysis ? If none, removing them from the beginning will allow your clusters to be more specific to your …
Answer: How to calculate cell type frequency between two groups in single cell data
by
Bastien Hervé
5.3k
I believe `sample_id` are your replicates in either `patient` or `control`. You can do it manually by normalizing the number of cells yo…
Answer: bfctools merge [E::hts_open_format] Failed to open file
by
j.f.akers
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I think the program is trying to open a .vcf.gz.csi file rather than the actual data which is the .vcf.gz file, the csi file is not data, j…
Comment: LDhat lookup table
by
NÚRIA
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Hi! Did you manage to fix this? I run convert successfully on 60 unphased diploid samples (1500bp), hence I used lktable available in LDh…
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It's Parkinson's disease. How do I get the right order?
Comment: How to scrape BioMart data from https://sorfs.ugent.be/ website
by
QX
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yes but they did not reply
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