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117,466 results • Page
3 of 2350
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
128
views
help with germline analysis using cnvkit
cnvkit
4 days ago by
ww22runner
▴ 60
2
votes
4
replies
278
views
Construction of a phylogentic tree for thousands of bacterial genomes
Phylogenomics
updated 4 days ago by
Mensur Dlakic
★ 27k • written 5 days ago by
biobiu
▴ 150
0
votes
2
replies
211
views
Adding a simple tag to VCF Info column
vcf
updated 4 days ago by
Ram
44k • written 4 days ago by
avelarbio46
▴ 30
0
votes
0
replies
138
views
PbJelly Resume
Gap-filling
PacBio
PbJelly
updated 4 days ago by
Ram
44k • written 5 days ago by
Lissa Cruz Saavedra
• 0
1
vote
1
reply
169
views
Automated methods for comparing trees
distance
agglomerative
compare
tree
updated 5 days ago by
Mensur Dlakic
★ 27k • written 5 days ago by
Alex Reynolds
35k
1
vote
3
replies
210
views
Pdb file isn't opening in the Desmond
Simulation
MD
5 days ago by
20212854117sakib
• 0
0
votes
4
replies
271
views
Bulk converting superseded TCGA UUIDs
R
TCGAutils
TCGA
updated 4 days ago by
Zhenyu Zhang
★ 1.2k • written 5 days ago by
loughrae
▴ 90
0
votes
1
reply
157
views
Are bam2fastq --no-aligned and samtools fastq -f 4 same?
samtools
assembly
spades
fastq
updated 5 days ago by
Pierre Lindenbaum
162k • written 5 days ago by
Yogesh
• 0
3
votes
3
replies
239
views
How to download Gene annotations (by Ensembl) track on NCBI Sequence Viewer 3.49.0
Sequence-Viewer
Ensembl
NCBI
updated 4 days ago by
Ram
44k • written 5 days ago by
rahu
• 0
0
votes
2
replies
191
views
Is it possible to access controlled TCGA data through TCGA Biolinks in R?
R
GDC
RStudio
TCGA
4 days ago by
Destiny
• 0
3
votes
2
replies
232
views
Seurat object with multiple PCAs/UMAPs from different assays
R
Seurat
updated 5 days ago by
bk11
★ 2.7k • written 5 days ago by
solo.albif
• 0
0
votes
2
replies
209
views
How to find column names for ENCODE ATAC-seq data?
encode
atac-seq
bed
updated 4 days ago by
Ming Tommy Tang
★ 4.0k • written 5 days ago by
DN99
▴ 20
0
votes
2
replies
833
views
miRNAs pathway analysis
pathway
miRNA
updated 5 days ago by
Daniel
• 0 • written 2.7 years ago by
zizigolu
★ 4.3k
5
votes
0
replies
129
views
Tool:
GeneScape: A Python package for gene ontology visualization
ontology
GO
5 days ago by
Istvan Albert
101k
3
votes
0
replies
169
views
Herald:
The Biostar Herald for Monday, June 10, 2024
herald
5 days ago by
Biostar
2.9k
0
votes
0
replies
115
views
CIBERSORTx error (error in rep(2, size * length(cells) -1)) : invalid 'times' argument
deconvolution
RNA-seq
CIBERSORTx
CIBERSORT
5 days ago by
Mr. George
• 0
0
votes
1
reply
156
views
Automated my docking results by using script
Receptor-ligand-interaction
DSV
VINA
updated 5 days ago by
Ram
44k • written 5 days ago by
iamsmor
• 0
0
votes
3
replies
304
views
gene expression design
R
gene-expression
RNA-seq
updated 4 days ago by
rfran010
▴ 950 • written 6 days ago by
bioinfo1994
• 0
2
votes
4
replies
364
views
QC Analysis from Sanger sequencing
qc
ab1
sanger
5 days ago by
davidmaimoun
▴ 50
1
vote
1
reply
184
views
How to calculate the Genetic Distance (P-Distance) by using mtDNA pacBio data?
pacBio
Genetic-Distance
mtDNA
4 days ago by
hashim.rana11
▴ 20
2
votes
3
replies
250
views
bash for merging bam files by samtools
samtools
updated 5 days ago by
GenoMax
143k • written 5 days ago by
QX
▴ 20
0
votes
1
reply
279
views
Extremely high variance of coverage for metagenomic sample (variance-to-mean ratio ~2.5)
MetaBAT
metagenome
coverage
5 days ago by
k-tarasov
• 0
0
votes
2
replies
2.9k
views
blastn_vdb "- Error opening the following db(s): "
sra
sra-toolkit
blast
blastn_vdb
wgs
updated 5 days ago by
cduvallet
• 0 • written 7.4 years ago by
musta1234
▴ 30
0
votes
0
replies
149
views
Tutorial:
SingleCellExperiment object explained with a real-world example
bioconductor
scRNA-seq
single-cell
updated 4 days ago by
Ram
44k • written 5 days ago by
Ming Tommy Tang
★ 4.0k
2
votes
2
replies
319
views
deeptools Compute reference-point and scale-regions
deeptools
computeMatrix
plotprofile
5 days ago by
RD
▴ 20
0
votes
3
replies
407
views
Clusters in Differential Gene Expression Data
gdc
gene-expression
seurat
updated 4 days ago by
Zhenyu Zhang
★ 1.2k • written 15 days ago by
Scofield
• 0
0
votes
1
reply
271
views
Exon count and GC content
Exon-count
GC-content
updated 5 days ago by
Pierre Lindenbaum
162k • written 9 days ago by
Varsha
• 0
2
votes
4
replies
438
views
Making heatmaps of ATACseq annotation data in R?
ATAC-seq
RStudio
updated 4 days ago by
rfran010
▴ 950 • written 9 days ago by
Ronin
▴ 10
2
votes
2
replies
212
views
What does the name of a read mean? How to find its location in genome viewer?
ukb
reads
updated 6 days ago by
Pierre Lindenbaum
162k • written 6 days ago by
sacryt
• 0
0
votes
3
replies
281
views
Detecting a virus in RNA-Seq Data
fastq-screen
Rna-seq
kraken2
updated 5 days ago by
rfran010
▴ 950 • written 6 days ago by
bioinfo1994
• 0
1
vote
2
replies
266
views
finding housekeeping genes and small RNA sequences of Arabidopsis thaliana
housekeeping-genes
RNA
3 days ago by
analyst
▴ 50
2
votes
2
replies
239
views
getting RNA-seq raw counts from Kallisto
counts
raw
RNA-seq
Kallisto
4 days ago by
Meghan.T
• 0
0
votes
0
replies
123
views
Difference in mapping rate when aligned with mapper.pl of miReep2 and bowtie1
miRNASeq
bowtie
RNASeq
miRDeep2
small
6 days ago by
MIKA
• 0
0
votes
1
reply
199
views
What database to use for GATK baseRecalibration when using the ensembl hg19 genome
ensembl
gatk
updated 6 days ago by
GenoMax
143k • written 7 days ago by
ramiro.barrantes
• 0
0
votes
1
reply
214
views
Design model matrix with limma with cell different proportions estimates and batch effect
R
limma
deconvolution
RNA-Seq
updated 6 days ago by
Gordon Smyth
★ 7.2k • written 7 days ago by
ij283
• 0
0
votes
1
reply
203
views
Looking for a scientific source talking about the functionality of CONCOCT and MetaBAT
sources
CONCOCT
assembly
METABAT
updated 1 day ago by
Jess
▴ 20 • written 7 days ago by
marie.harmel
▴ 10
0
votes
8
replies
590
views
Rstudio hangs on logisic regression using generalized estimating equations (geepack::geese())
geepack
updated 2 days ago by
Ram
44k • written 7 days ago by
jonas.andersson
▴ 30
0
votes
6
replies
398
views
Network analysis of TCGA and GTEx gene expression datasets
R
GTEx
studio
TCGA
updated 6 days ago by
marco.barr
▴ 150 • written 7 days ago by
Nusrat
• 0
4
votes
7
replies
381
views
fastq-dump not working in loop
fastq-dump
updated 7 days ago by
Ram
44k • written 7 days ago by
analyst
▴ 50
3
votes
5
replies
331
views
assemble extracted kmers into longer contigs/sequences
assembly
unique
kmers
7 days ago by
sapuizait
▴ 10
3
votes
4
replies
320
views
Error: Trimmomatic Command not found
NGS
Illumina
Quality-Control
Trimmomatic
updated 7 days ago by
Ram
44k • written 8 days ago by
Tundup
• 0
0
votes
1
reply
224
views
single nucleus RNA seq processing pipeline questions
demultiplexing
snRNAseq
updated 7 days ago by
dsull
★ 6.2k • written 8 days ago by
biotrekker
▴ 100
0
votes
0
replies
184
views
Add gene expression boxplot from plotCounts to each row of oncoprint via ComplexHeatmap
R
ComplexHeatmap
oncoprint
updated 7 days ago by
Ram
44k • written 8 days ago by
bioinfo8
▴ 230
0
votes
1
reply
217
views
Hybrid ScRNA Seq genome (transcriptome
scrna
10x
cellranger
updated 6 days ago by
dsull
★ 6.2k • written 8 days ago by
Kay
• 0
0
votes
1
reply
202
views
Fastqc: kmer-content failed
fastqc
kmer
updated 7 days ago by
Ram
44k • written 8 days ago by
Joseph
• 0
5
votes
5
replies
432
views
Home made clustering
R
clustering
8 days ago by
Bastien Hervé
5.4k
4
votes
9
replies
555
views
How to solve Freebayes memory issue
NGS
freebayes
SNP
7 days ago by
anikcropscience
▴ 260
5
votes
3
replies
334
views
chIP-seq vs ATACseq analysis
ATACseq
5 days ago by
QX
▴ 20
0
votes
0
replies
368
views
How to calculate the P-distance in Heteroplasmy Analysis Using mtDNA PacBio Data: Tools and Procedures
pacBio
Heteroplasmy
Somatic-mutations
mtDNA
updated 7 days ago by
Ram
44k • written 8 days ago by
hashim.rana11
▴ 20
1
vote
1
reply
232
views
Fastq files from control WGS X30 samples, Illumina Novaseq 6000
dna-seq
wgs
fastq
updated 7 days ago by
Ram
44k • written 8 days ago by
damian.loska
▴ 20
117,466 results • Page
3 of 2350
Recent Votes
Comment: bash for merging bam files by samtools
Alignment tool for very short reads (25bp)
Answer: edgeR batch effect model matrix sanity check
Answer: edgeR batch effect model matrix sanity check
Answer: Failed to download data from EBI with ascp
Alignment tool for very short reads (25bp)
Answer: Overrepresented sequence in reverse read
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Recent Replies
Comment: how linearize nucleotide lines in axt file
by
resug
▴ 30
There are two sequences per entry, and the provided awk script has merged the two sequences into a single linear sequence. But the objectiv…
Answer: how linearize nucleotide lines in axt file
by
GenoMax
143k
Using @yokofakun 's [**linearize fasta code**][1] awk '/^Lm/ {printf("%s%s\t",(N>0?"\n\n":""),$0);N++;next;} {printf("%s",$0);} END …
Comment: Help aligning Nanopore Long Read RNA seqs
by
WouterDeCoster
47k
That is very few reads. Are you sure your run was successful?
Comment: Alignment tool for very short reads (25bp)
by
ATpoint
83k
bowtie aka bowtie1 was developed when these very short reads were state of the art. Id give that a try and see what comes out. Multithreade…
Answer: Alignment tool for very short reads (25bp)
by
Jeremy Leipzig
22k
> What are other reliable tools for the alignment of DNA reads with very short lengths (25-50bp)? [vmatch][1] [1]: http://www.vma…
Comment: edgeR batch effect model matrix sanity check
by
kmyers2
▴ 80
Thank you! Appreciate your reply!
Comment: blast Segmentation fault
by
Tina
• 0
I used 'blastn-short', but it still resulted in a segmentation fault. I downloaded the 'nt_euk' index from NCBI ([enter link description he…
Comment: Help aligning Nanopore Long Read RNA seqs
by
sewaw37819
• 0
> What percentage of your library do you expect to be "long-non-coding transcripts"? A higher percentage than what we are seeing right now…
Comment: Failed to download data from EBI with ascp
by
Michael
54k
Please check my answer. No need to send an email to EBI either.
Answer: Failed to download data from EBI with ascp
by
Michael
54k
**Anonymous Aspera download from ENA works as expected.** Please follow the official documentation https://ena-docs.readthedocs.io/en/late…
Answer: Alignment tool for very short reads (25bp)
by
Jack Tierney
▴ 360
Kudos for writing such a clear and well formatted question. I will give my perspective but don't claim to be an authority. Full disclosure …
Comment: Failed to download data from EBI with ascp
by
ATpoint
83k
Please email EBI and dont post duplicates. Especially not as an answer.
Comment: Help aligning Nanopore Long Read RNA seqs
by
rfran010
▴ 950
What percentage of your library do you expect to be "long-non-coding transcripts"? > (though there IS some coverage, but mostly on whole…
Comment: Overrepresented sequence in reverse read
by
Jaskaran Singh
• 0
Thank You so much....it was really helpful...i was able to remove the poly G with fastp
Comment: Overrepresented sequence in reverse read
by
Jaskaran Singh
• 0
Hi, Thanks, it was helpul information. I used fastp to remove the poly g and the QC seems to be fine now.
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