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Limit : this month
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537 results • Page
2 of 11
Sort: Votes
Rank
Views
Votes
Replies
2
votes
5
replies
428
views
Marking duplicates using UMIs
Deduplication
UMI
updated 2 days ago by
i.sudbery
19k • written 4 days ago by
Lipika
• 0
2
votes
5
replies
676
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 4 days ago by
Jesse
▴ 740 • written 5 days ago by
Ann
★ 2.4k
2
votes
2
replies
258
views
How to row normalize a matrixplot?
scRNA-seq
RNA-seq
single-cell
scanpy
9 days ago by
bioinfo
▴ 150
2
votes
4
replies
392
views
Per Base Sequence Content - continuous raise of G%
fastqc
updated 14 days ago by
GenoMax
141k • written 15 days ago by
pl.terzian
• 0
2
votes
0
replies
1.8k
views
ComBat-seq adjustment of batch effects
RNA-Seq
ComBat-seq
SVA
edgeR
batch-effect
updated 8 days ago by
Ram
43k • written 3.4 years ago by
chatterjee.arumoy
▴ 50
2
votes
6
replies
397
views
create a gene count matrix csv file from seurat object
Seurat
sparseMatrix
16 days ago by
jkim
▴ 170
2
votes
3
replies
3.0k
views
RNA-seq batch effect correction
RNA-Seq
batch-effect
sequencing
updated 6 days ago by
Ram
43k • written 6.9 years ago by
endikavarela
• 0
2
votes
2
replies
1.6k
views
read count for RNA sequencing via nanopore
long-reads
RNA-seq
gene-expression
read-count
updated 19 days ago by
Ram
43k • written 2.9 years ago by
gat
• 0
2
votes
6
replies
629
views
Overlapping and merging ChIP-seq peaks
MACS2
HOMER
ChIP-seq
peak-calling
updated 22 days ago by
Ram
43k • written 4 months ago by
zea
• 0
2
votes
3
replies
279
views
Extracting information from my VCF file
VCF
updated 29 days ago by
bioruffo
▴ 40 • written 29 days ago by
realtreeecat
• 0
2
votes
2
replies
271
views
DepMap: siRNA and CRSIPR discrepancy
DepMap
updated 13 days ago by
ATpoint
82k • written 13 days ago by
Shicheng Guo
★ 9.4k
2
votes
7
replies
805
views
Removing duplicates
duplicates
ONT
minimap2
updated 6 days ago by
joe
▴ 510 • written 7 days ago by
quentinperriere
• 0
2
votes
5
replies
435
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats
hg002
bed
homopolymer-regions
8 days ago by
Bikram Kumar
• 0
2
votes
10
replies
819
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 27 days ago by
Ram
43k • written 9 weeks ago by
Sky
▴ 10
2
votes
9
replies
798
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 1 day ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
2
votes
5
replies
668
views
samtools mpileup taking too long
Bam
samtools
sam
alignment
updated 19 days ago by
Ram
43k • written 6 weeks ago by
K
• 0
2
votes
4
replies
239
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
23 hours ago by
samuelkalandarov2002
▴ 10
2
votes
18
replies
1.6k
views
error when running phg create-maf-vcf to build a built practical haplotype graph (v2)
pangenome
phg_v2
plants
PHG
22 days ago by
b.contreras.moreira
▴ 170
2
votes
3
replies
253
views
P-value Threshold Consideration in Multi-Sample RNA-Seq Experiment
statistics
RNA-Seq
p-value
updated 22 days ago by
Ram
43k • written 23 days ago by
Netanel
• 0
2
votes
3
replies
1.1k
views
Polishing PACBIO corrected assembly using ONT and ILLUMINA data (.fastq)
fasta
Nanopore
long-read
fastq
updated 19 days ago by
Ram
43k • written 2.8 years ago by
K
▴ 10
1
vote
0
replies
149
views
Contradictions in GSEA results
GSEA
Enrichment-analysis
PEA
updated 27 days ago by
Ram
43k • written 27 days ago by
Tolga
▴ 30
1
vote
2
replies
269
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 7 days ago by
Ram
43k • written 7 days ago by
aniigodwinn
• 0
1
vote
3
replies
229
views
some error in building kraken2 database
metagenome
kraken2
1 day ago by
Art1ess
• 0
1
vote
3
replies
190
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
1 day ago by
WouterDeCoster
47k
1
vote
1
reply
459
views
PLINK multivariable GLM output: p-value without BETA and SE
linear-model
glm
plink
updated 16 days ago by
chrchang523
10k • written 16 days ago by
dsbusiness135
▴ 10
1
vote
2
replies
207
views
Flow Cytometry Data Analysis by Seurat
Seurat
updated 27 days ago by
Ram
43k • written 27 days ago by
gdfsnkfns
• 0
1
vote
0
replies
537
views
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers
TRINITY
5 days ago by
mathavanbioinfo
▴ 90
1
vote
1
reply
174
views
Failed to download data from EBI with ascp
EBI
aspera
updated 13 days ago by
GenoMax
141k • written 14 days ago by
biock
▴ 60
1
vote
7
replies
888
views
GATK Mutect2 Input files reference and features have incompatible contigs: No overlapping contigs found.
hg19
Mutect2
GATK
Variant-Calling
updated 29 days ago by
Ram
43k • written 9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
1
vote
3
replies
253
views
CCA with random effects model
CCA
updated 22 days ago by
dariober
14k • written 23 days ago by
leranwangcs
▴ 120
1
vote
1
reply
175
views
Help/Direction Needed for Data Analysis of RNA
Sequencing
RNA-seq
DNA-Seq
updated 8 days ago by
dsull
★ 5.8k • written 8 days ago by
niruf
• 0
1
vote
2
replies
283
views
Tumour purity and ploidy estimation
Copy-number
Whole-exome-sequencing
8 days ago by
bp22
▴ 80
1
vote
1
reply
190
views
Tool for gene function identification
Gene-Function
updated 22 days ago by
Ram
43k • written 23 days ago by
Estevão
• 0
1
vote
3
replies
349
views
how to do the repeatability filtering of vcf files?
snp
vcf.
updated 23 days ago by
Pierre Lindenbaum
161k • written 24 days ago by
Max
• 0
1
vote
0
replies
155
views
DESeq2 comparing timepoints within treatment and account for background control change
RNAseq
DEG
DESeq2
updated 13 days ago by
Ram
43k • written 13 days ago by
ian.will
▴ 30
1
vote
0
replies
367
views
Differential expression analysis on multiple integrated datasets
microarray
Z-score
limma
differential-gene-expression
meta-analysis
updated 15 days ago by
Ram
43k • written 2.4 years ago by
michael.s
▴ 10
1
vote
2
replies
808
views
What type of normalization does removeBatchEffect function require as the input?
batch
limma
removeBatchEffect
rna-seq
batch-effect
updated 8 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
1
vote
2
replies
1.0k
views
An issue with application of SPAdes genome assembly in Galaxy
Galaxy
SPAdes
updated 22 days ago by
Ram
43k • written 2.4 years ago by
adnan.lahuf
• 0
1
vote
3
replies
344
views
Ensembl gene id conversion
biomart
ensembl
updated 8 days ago by
ATpoint
82k • written 10 days ago by
naveedhasan2000
• 0
1
vote
3
replies
4.1k
views
Evaluating removing batch effect tools with PCA or MDS?
bioconductor
limma
sva
r
batch-effect
updated 6 days ago by
Ram
43k • written 7.6 years ago by
Lluís R.
★ 1.2k
1
vote
2
replies
821
views
Replacing default numbers with geneNames in enhancedVolcano
EnhancedVolcano
updated 22 days ago by
Ram
43k • written 2.6 years ago by
Mohan
• 0
1
vote
2
replies
921
views
vg surject for long reads
long-reads
vg
variation-graph
surject
updated 19 days ago by
Ram
43k • written 23 months ago by
ved_vyas
▴ 10
1
vote
4
replies
807
views
I want to calculate if the sample has whole genome duplication event or not?
sequencing
wgs
15 days ago by
Hyper_Odin
▴ 310
1
vote
3
replies
6.1k
views
Error for converting from gene symbol to Entrez IDs
Entrez-ID
org.Dr.eg.db
updated 8 days ago by
Ram
43k • written 5.5 years ago by
modarzi
▴ 170
1
vote
2
replies
264
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq
kallisto
8 days ago by
bioinfo
▴ 150
1
vote
2
replies
325
views
BAM to CRAM and BAM recover with smaller size
BAM
samtools
CRAM
updated 21 days ago by
jkbonfield
★ 1.2k • written 5 weeks ago by
geocarvalho
▴ 360
1
vote
2
replies
625
views
Nanopore multisample variant calling
SNPs
nanopore
SNP-calling
variants
multisample
26 days ago by
colindaven
6.4k
1
vote
2
replies
257
views
Is it possible to see so little adipocyte in white adipose tissue?
scRNA-seq
29 days ago by
kayah
• 0
1
vote
4
replies
278
views
Removing batch effect using combat-seq
batch
effect
RNA-Seq
combat-seq
updated 23 days ago by
BioinfGuru
★ 1.7k • written 23 days ago by
Netanel
• 0
1
vote
0
replies
1.1k
views
interpretation of trajectory and batch effect
monocle3
batch-effect
trajectory
updated 16 days ago by
Ram
43k • written 3.5 years ago by
tushard1987
▴ 10
537 results • Page
2 of 11
Recent Votes
Comment: Adding CB tag to bam file
Comment: alignment result
Comment: clustalo - align milions of short seq, memory issue
Answer: clustalo - align milions of short seq, memory issue
Comment: downloading genomes in fasta format from accession ids
Comment: PCA plot (Suggestions Needed)
Answer: PCA plot (Suggestions Needed)
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Recent Replies
Comment: Adding CB tag to bam file
by
Pierre Lindenbaum
161k
samtools addreplacerg is for read groups. This is not what OP asked.
Comment: Adding CB tag to bam file
by
Maria
• 0
When I try ``` samtools addreplacerg -r "@CB\tID:$cell" -o $cell.bam $LINE``` the CB tag gets add to the header, but the tag in every line …
Answer: Figures are disappeared from html report of SnpEff
by
Pierre Lindenbaum
161k
the remote website providing the javascript or/and the images is down or you're now behind a proxy. Check the firefox console: https://fire…
Comment: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
ah ! and your code doesn't work because clinvar ID is not a rs-ID.
Answer: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
$ cat input.rs rs11203366 rs11203367 rs874881 rs776453694 rs80324279 rs324420 rs112766203 wget -…
Comment: Highest variable features in single cell data
by
ATpoint
82k
> and these cells are not even in a single cluster. What does this mean? If you run clustering on all cells then every cell is assigned t…
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas
by
Bertalan_Takacs
▴ 90
Yes, I can tell that, but as far as I see it doesn't contain any other information about the genomes, such as if they were representative i…
Answer: Hide positions in alignment with 99% "–" characters to ignore single sequence in
by
b.contreras.moreira
▴ 170
You can try <https://github.com/inab/trimal>
Comment: To get p-values for the TPM
by
VITALA
• 0
yes i want what rsem does and i did try with prior-enhanced option/pRSEM, but i think pRSEM is for chipseq data
Comment: alignment result
by
ahmad.sajad4541
• 0
Thank you so much. Should i proceed for annotation step?
Comment: PCA plot (Suggestions Needed)
by
swbarnes2
14k
The code you already posted in the bioconductor board had simulated data, and the PCA image is the same.
Answer: Network Alignment
by
Scooter
▴ 280
Unfortunately, it's not working for me either, and the web site doesn't exist anymore. You might try reaching out to the authors, but I kn…
Answer: How could I generate a gi_taxid_nucl.dmp file similar to the one previously host
by
ZhangYuanfeng
• 0
JUST GIVE THE ANSWER! Here is the solution: ```bash aria2c -c -s 4 -j 4 \ https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/pd…
Comment: PCA plot (Suggestions Needed)
by
Aaliya
▴ 10
I have actually used DESeq2 data.
Comment: Why cd-hit-est not work when sequence identity threshold<0.95?
by
Dateline
• 0
So, why? I have 18GB of data, and when -c=0.95, the run ends in about two days, while when -c=0.9, it has been three days and only a little…
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