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119,827 results • Page
1 of 2397
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Votes
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0
votes
0
replies
15
views
Script that should show if the position of an indel is within the range of a miRNA is creating empty files. Could you help me?
script
1 hour ago by
jhonatan.henrique
• 0
1
vote
1
reply
294
views
Issues with RAT in CAT_pack and Optimizing Relative Abundance Calculation
metagenomics
taxonomy
mag
annotation
updated 2 hours ago by
mks002
▴ 220 • written 8 weeks ago by
LuciaNhu
▴ 10
0
votes
1
reply
62
views
Hi-C interactions significance
chromatin
interactions
pvalue
Hi-C
significance
updated 3 hours ago by
hamarillo
▴ 80 • written 6 hours ago by
Helena
• 0
2
votes
3
replies
265
views
Conceptual and statistical help in creating a synthetic RNAseq cohort from a real-world cohort of samples
statistics
DESeq2
RNAseq
updated 20 minutes ago by
Gordon Smyth
★ 7.7k • written 2 days ago by
K.patel5
▴ 150
0
votes
0
replies
37
views
StringTie error
DE
count
analysis
StringTie
RNA-seq
4 hours ago by
SHN
▴ 40
821
votes
169
replies
160k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 12 weeks ago by
Biostar
3.2k • written 8.0 years ago by
Istvan Albert
102k
0
votes
0
replies
27
views
A problem with a plink file made from a VCF
plink
vcf
4 hours ago by
HoWI
• 0
0
votes
0
replies
33
views
Annotating bacterial intergenic regions
bacteria
gene
intergenic
annotation
5 hours ago by
Gio
• 0
0
votes
0
replies
44
views
KEGGREST to retrieve some data from KEGG
genes
keggLink
9 hours ago by
mrashad
▴ 80
1
vote
1
reply
93
views
Creating adjacency matrix from collapsed row values in R
adjacency
reshape2
matrix
r
10 hours ago by
ARP
• 0
0
votes
0
replies
54
views
Blast with variable number of Ns
blast
7 hours ago by
samuel.himes
• 0
1
vote
5
replies
352
views
Deducing AIRR-seq Library Generation From SRA Data
generation
SRA
airflow
primer
airrflow
10 hours ago by
A Soggy Waffle
• 0
2
votes
1
reply
110
views
BWA align in human and parasite genome, and sort them
BWA
updated 12 hours ago by
GenoMax
148k • written 15 hours ago by
Bender
• 0
1
vote
3
replies
150
views
Use of "grep" in RNAseq trimming
RNAseq
PolyA
updated 12 hours ago by
GenoMax
148k • written 15 hours ago by
Luna_1215
• 0
0
votes
2
replies
137
views
Could someone send me CISA software ?
me
HELP
1 hour ago by
lu_baicheng
• 0
0
votes
1
reply
93
views
Download metabolic information from databases using the NCBI Taxonomy ID
metabolism
database
R
taxonomy
ncbi
updated 12 hours ago by
GenoMax
148k • written 14 hours ago by
ThaiosX195
• 0
0
votes
1
reply
82
views
No change in quality score graph even after adapter removal
rna-seq
fastqc
Trimmomatic
updated 15 hours ago by
dsull
★ 7.0k • written 15 hours ago by
Sreedevi
• 0
0
votes
0
replies
54
views
Regarding ClinVar's VCF file
matrix
disease
vcf
clinvar
gene
15 hours ago by
singhankit973
• 0
1
vote
4
replies
141
views
Single-cell dimensionality reduction and clustering
Seurat
updated 16 hours ago by
Michael
55k • written 18 hours ago by
xingyu
▴ 10
0
votes
0
replies
52
views
How to load series matrix file into SeSAMe or minfi for processing?
sesame
geo
illumina
minfi
machine-learning
updated 8 hours ago by
Ram
44k • written 16 hours ago by
Junk
• 0
0
votes
1
reply
79
views
Plant diploid genome, phashed, CLR reads, PECAT
diploid
genome
Phased
1 hour ago by
sansan96
▴ 130
0
votes
1
reply
114
views
How should I integrate the h5 files of multiple samples in order to implement hdWGCNA?
Seurat
hdWGCNA
scRNA-seq
updated 16 hours ago by
Bastien Hervé
6.0k • written 1 day ago by
Apprentice
▴ 170
4
votes
14
replies
2.5k
views
7 follow
Is there anyone who downloaded Azimuth packges?
Azimuth
scRNAseq
updated 11 hours ago by
ATpoint
86k • written 9 months ago by
kayah
▴ 20
2
votes
10
replies
375
views
Error in conversion of ensembl to gene names
Ensembl
BioMart
updated 7 hours ago by
Istvan Albert
102k • written 1 day ago by
anasjamshed
▴ 140
1
vote
1
reply
343
views
Tool:
CellLocator: An Open-Source Tool for Unlocking Deeper Insights from Live-Cell Imaging
open-source
deep-learning
denoising
single-cell
incucyte
1 day ago by
Michael
▴ 10
0
votes
3
replies
200
views
Which data to choose for correlation examination
correlation
WGCNA
TPM
batch
spearman
1 day ago by
lyan125
▴ 10
4
votes
12
replies
375
views
Transcript coverage 3' bias. Is it really that determining?
mappings
transcriptome
RNA
updated 13 hours ago by
i.sudbery
20k • written 1 day ago by
Amb@r85
▴ 10
3
votes
7
replies
545
views
Quantify miRNAs from whole transcriptome library (single end, TruSeq, 100bp)
miRNA
whole-transcriptome-TruSeq
updated 1 day ago by
i.sudbery
20k • written 4 months ago by
w.denhollander
• 0
0
votes
1
reply
165
views
comparing STARsolo UMI-based directional deduplication vs umi-tools?
single-cell
starsolo
deduplication
umi-tools
updated 1 day ago by
i.sudbery
20k • written 2 days ago by
mk
▴ 300
0
votes
0
replies
96
views
Prediction of sRNA in FASTA file
FASTA
Prediction
sRNA
1 day ago by
nashwaabdulrasheed09
• 0
0
votes
0
replies
94
views
Identification of SSR markers from RNA-seq data
MISA
SSR-markers
data
RNA-seq
1 day ago by
Kutti
• 0
0
votes
8
replies
509
views
Super enhancer calling using ROSE for mm39 genome: list index out of range error
ChIP-Seq
super-enhancers
ROSE
mm39
updated 10 hours ago by
jared.andrews07
★ 18k • written 3 days ago by
Gayatri
• 0
2
votes
4
replies
265
views
Which method should I use to merge scRNA-seq data, Cellranger aggr or Seurat?
Ranger
Cell
hdWGCNA
Seurat
scRNA-seq
1 day ago by
Apprentice
▴ 170
0
votes
1
reply
145
views
assembling human mitochondrial genomes with nanopore long reads
ONT
assembly
genome
mitochondria
nanopore
1 day ago by
eebloom
▴ 90
5
votes
12
replies
6.3k
views
how can i download human ribosomal reference ?
RNA-Seq
rRNA
updated 1 day ago by
tomas4482
▴ 430 • written 5.6 years ago by
sabaghianamir70
▴ 70
2
votes
4
replies
279
views
How should the order of microbiome data preprocessing be prioritized?
aggregation
microbiome
preprocess
normalization
filter
1 day ago by
ssko
▴ 20
6
votes
10
replies
861
views
6 follow
High Detection of Duplication in RNAseq dataset
Deduplication
RNAseq
updated 1 day ago by
i.sudbery
20k • written 3 months ago by
karlensberg
• 0
0
votes
6
replies
760
views
What should I do if death cell counts and types biologically important in my single cell data?
scRNA
cell-death
single-cell
updated 1 day ago by
i.sudbery
20k • written 12 weeks ago by
carolofharvest
▴ 50
0
votes
1
reply
385
views
Salmon low mapping rates
Reference
Mapping
Salmon
RNA-seq
updated 2 days ago by
jnechacov
• 0 • written 6 months ago by
L.Chang
• 0
0
votes
3
replies
437
views
Removing gDNA contamination from RNA seq data
contamination
gDNA
updated 1 day ago by
i.sudbery
20k • written 3 months ago by
yahav.bracha
• 0
0
votes
2
replies
232
views
dorado and modkit for m6A identification
dorado
m6A
modkit
2 days ago by
baibhu1234
• 0
0
votes
0
replies
109
views
cnvkit results with start positions always 0 ?
cnvkit
variant-calling
updated 2 days ago by
Ram
44k • written 2 days ago by
ank
• 0
0
votes
0
replies
113
views
Regression and scaling in scanpy
scanpy
2 days ago by
bioinfo
▴ 150
0
votes
2
replies
179
views
Question about metabolic pathway prediction using only DNA sequencing data
metabolism
genomics
ngs
updated 2 days ago by
hakimbazol
▴ 40 • written 2 days ago by
Mark
▴ 20
1
vote
6
replies
284
views
English terms distinguishing genotype allelic nucleotides (T/C) from VCF encoded genotype (0/1)
genotypes
vcf
2 days ago by
Jeremy Leipzig
22k
0
votes
0
replies
114
views
How to define a clonotype by its TCR sequencing data with its own structure.
TCR
sequencing
clonotype
scRNA
2 days ago by
diqixiaoyaoer
▴ 20
3
votes
3
replies
263
views
Getting fasta sequence for a gene
fasta
regulatory
genome
region
gene
updated 2 days ago by
Istvan Albert
102k • written 2 days ago by
zizigolu
★ 4.3k
0
votes
3
replies
164
views
Identification of variants from Spatial Transcriptomics using STARSolo
spatial-transcriptomics
STAR
visium
updated 2 days ago by
Ram
44k • written 2 days ago by
kanika.151
▴ 160
0
votes
6
replies
332
views
Seurat Mito Prefix Removed from Features
Seurat
updated 1 day ago by
yura.grabovska
▴ 690 • written 3 days ago by
Koki
• 0
0
votes
1
reply
183
views
Is there a way to write a genbank file in R?
R
Genbank
Genetics
BioConductor
updated 2 days ago by
yura.grabovska
▴ 690 • written 3 days ago by
Jack
• 0
119,827 results • Page
1 of 2397
Recent Votes
Comment: Transcript coverage 3' bias. Is it really that determining?
Comment: Transcript coverage 3' bias. Is it really that determining?
Answer: Transcript coverage 3' bias. Is it really that determining?
Answer: BWA align in human and parasite genome, and sort them
Issues with RAT in CAT_pack and Optimizing Relative Abundance Calculation
Comment: Conceptual and statistical help in creating a synthetic RNAseq cohort from a rea
Answer: Sort VCF File by Position?
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Recent Replies
Comment: Plant diploid genome, phashed, CLR reads, PECAT
by
sansan96
▴ 130
Thanks so much.
Comment: Could someone send me CISA software ?
by
lu_baicheng
• 0
yes,but i do need this special software to handle my data.
Answer: Issues with RAT in CAT_pack and Optimizing Relative Abundance Calculation
by
mks002
▴ 220
Hi Nhu, Since you are running the CAT_pack in "--mode cr", it would ask for the classification file and it seems you have provided that.…
Answer: Hi-C interactions significance
by
hamarillo
▴ 80
http://homer.ucsd.edu/homer/interactions/HiCinteractions.html https://www.nature.com/articles/ncomms15454
Answer: Conceptual and statistical help in creating a synthetic RNAseq cohort from a rea
by
Gordon Smyth
★ 7.7k
Sorry, this whole process makes no sense to me at all. From a speed point of view, why would you not run a faster method like limma-voom o…
Comment: Super enhancer calling using ROSE for mm39 genome: list index out of range error
by
jared.andrews07
★ 18k
The warnings can be safely ignored, they are due to the TxDb containing many seqlevels not found in your peaks object. It is on the list to…
Answer: Creating adjacency matrix from collapsed row values in R
by
ARP
• 0
If anyone else comes across this issue, I found a way to solve it by creating a list from each of the vectors in X2 and using the solution …
Answer: Deducing AIRR-seq Library Generation From SRA Data
by
A Soggy Waffle
• 0
I found useful resources for immunoglobulin sequences and primers. Putting them here if some future traveler stumbles onto this post. Als…
Comment: Could someone send me CISA software ?
by
ATpoint
86k
If the website is not even available then find an alternative. Nothing gained from trying to make absolute abandonware work.
Comment: Is there anyone who downloaded Azimuth packges?
by
ATpoint
86k
I just tried and it worked beautifully. If you have issues then try to find the root, such uncustom and manual installation with forced res…
Comment: Is there anyone who downloaded Azimuth packges?
by
pariapooyan
• 0
This one had not worked for me as well.
Comment: Download metabolic information from databases using the NCBI Taxonomy ID
by
GenoMax
148k
Using [**EntrezDirect**][1] you can easily get the name of the organism $ esearch -db taxonomy -query "1354[taxID]" | esummary | xtrac…
Answer: BWA align in human and parasite genome, and sort them
by
GenoMax
148k
> I thought I would get same result From method 1 is got 60M .sorted.dup.pf.bam and grom method 2 I got .sorted.dup.bam 1.5GB. I want reas…
Answer: Use of "grep" in RNAseq trimming
by
GenoMax
148k
Please use a proper program that is aware of the fastq format. `BBMap suite` includes `polyfilter.sh` which will be the best option if you …
Comment: Odd behaviour - NCBI Eutils
by
GenoMax
148k
Only way would be to report this to NCBI help desk. They will respond but be ready to wait for a few business days.
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