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121,736 results • Page
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0
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31
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Rust-HTSlib Script Only Outputs BAM Header, Records Are Missing
Rust
BAM
rust_htslib
2 hours ago by
plusone
• 0
0
votes
0
replies
63
views
Single cell multiomics data i.e, sc(RNA+ATAC) seq data tar file
single
omics
cell
multi
updated 11 hours ago by
GenoMax
153k • written 12 hours ago by
Rupanjali
• 0
4
votes
3
replies
175
views
Running metaSPAdes with 71M paired-end reads: RAM and swap memory concerns
metaspades
assembly
metagenomics
updated 8 hours ago by
Mensur Dlakic
★ 29k • written 20 hours ago by
sumah.1si21bt017
▴ 20
0
votes
1
reply
844
views
Which metric is best to represent cell-level counts/features in Seurat: raw/log-normalized (nCount_RNA/nFeature_RNA) or SCTransform (nCount_SCT/nFeat…
R
visualization
updated 21 hours ago by
ATpoint
89k • written 8 days ago by
solo.albif
• 0
0
votes
2
replies
548
views
Job:
Help with bioinformatics/genetics content of my CV
terminology
CV
updated 1 day ago by
Anchal
• 0 • written 8 days ago by
mairena.hirschberg
• 0
845
votes
170
replies
185k
views
112 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
3.6k • written 8.7 years ago by
Istvan Albert
103k
5
votes
5
replies
254
views
how to download gene annotation for NCBI GENE ID
R
entrez
NCBI
updated 18 hours ago by
GenoMax
153k • written 1 day ago by
Bioinfonext
▴ 470
0
votes
1
reply
139
views
Where can I get Human microbiome dataset
microbiome
human
data
updated 1 day ago by
GenoMax
153k • written 1 day ago by
Emily
▴ 70
0
votes
8
replies
294
views
chimeraTE GTF format error
chimeraTE
22 hours ago by
frarodmar17
• 0
4
votes
5
replies
380
views
Estimating copy number of heterologous genes from WGS data in Yarrowia lipolytica
wgs
CNVs
copy-number
updated 1 day ago by
GenoMax
153k • written 3 days ago by
Giorgia
• 0
0
votes
0
replies
91
views
News:
online course (4th edition): Structural Variant Detection & Comparison
LongReads
Nanopore
PacBio
StructuralVariations
1 day ago by
Physalia-courses
★ 2.6k
1
vote
0
replies
107
views
News:
Cellosaurus release 53 + new SPARQL/RDF functionalities
database
biocuration
line
knowledgebase
cell
1 day ago by
Amos Bairoch
▴ 140
0
votes
1
reply
208
views
Relative viral load estimation from NGS data – is it possible?
virology
updated 1 day ago by
Jeremy Leipzig
23k • written 2 days ago by
omicon
▴ 40
0
votes
0
replies
132
views
Best Practice for Group Composition Plots in Phyloseq
phyloseq
microbiome
relative-abundance
2 days ago by
bioinfo
▴ 60
0
votes
1
reply
176
views
primer
primer
updated 2 days ago by
GenoMax
153k • written 2 days ago by
elahe
• 0
0
votes
0
replies
123
views
Help installing and running PITA & PicTar for miRNA target prediction
microRNA
PITA
PicTar
updated 2 days ago by
Ram
45k • written 2 days ago by
Andie
• 0
1
vote
1
reply
182
views
Splitting VCF using phase information
phasing
bcftools
vcf
updated 2 days ago by
cmdcolin
★ 4.3k • written 2 days ago by
Kyra
• 0
0
votes
0
replies
136
views
Generating VCF file from Illumina MEGA array
strand
VCF
SNP
illumina
microarray
2 days ago by
112233
• 0
3
votes
1
reply
192
views
High discrepancy between mutation frequency values
MF
AF
gnomAD
TCGA
updated 2 days ago by
Aleksandra
▴ 100 • written 2 days ago by
Ana
▴ 10
7
votes
3
replies
308
views
How to troubleshoot strange hyperparameter trace from BSLMM (GEMMA)
gemma
gwas
bslmm
updated 2 days ago by
Aleksandra
▴ 100 • written 3 days ago by
gina.maria
▴ 40
0
votes
1
reply
177
views
Mean count in DESeq
in
DESeq
count
Mean
updated 2 days ago by
GenoMax
153k • written 2 days ago by
prerna
• 0
6
votes
10
replies
455
views
is there publicly available tool for assembly of bionano data
OM
bionano
assembly
alignment
updated 2 days ago by
GenoMax
153k • written 2 days ago by
eebloom
▴ 110
3
votes
4
replies
7.5k
views
7 follow
Any bacterial databases that contain Gram staining information?
gram-positive
gram-negative
written 9.1 years ago by
archaeopteryx
• 0
0
votes
1
reply
839
views
detectRUNS R package error
mapping
detectRUNS
R
ROH
homozygosity
updated 2 days ago by
Miika
• 0 • written 3.0 years ago by
Roisin Marie
• 0
3
votes
1
reply
188
views
Visualisation of big insertions by using Illumina emedgene
emedgene
updated 2 days ago by
GenoMax
153k • written 3 days ago by
Nina
▴ 30
2
votes
5
replies
357
views
Integrity of bam files
integrity
RAN-seq
bam
samtools
2 days ago by
SHN
▴ 40
0
votes
0
replies
170
views
News:
Course: RNA Sequencing Data with R/Bioconductor - online, 3–14 November
RNAseq
DifferentialExpressionAnalysis
R
Bioconductor
2 days ago by
Physalia-courses
★ 2.6k
0
votes
2
replies
1.2k
views
Clumping- cannot mtfrm
clumping
MR
updated 3 days ago by
Onyeubani
▴ 90 • written 7 months ago by
sp
• 0
0
votes
0
replies
163
views
Covariate-adjusted SPIEC-EASI
microbiome
network
spieceasi
3 days ago by
b
• 0
0
votes
2
replies
286
views
What is the best practice for scRNAseq analysis of multiple samples?
scRNAseq
seurat
single
cell
3 days ago by
Tundup
▴ 10
0
votes
0
replies
203
views
Forum:
Trying to get into Drug Design & Molecular Docking
Docking
Biochemistry
Ligands
updated 3 days ago by
Ram
45k • written 4 days ago by
Shreyas
• 0
0
votes
2
replies
288
views
DESeq2 - Changing the order of counts / metadata
counts
metadata
DESeq2
updated 4 days ago by
GenoMax
153k • written 4 days ago by
himanshu0102
• 0
9
votes
7
replies
2.9k
views
Marker genes of hematopoietic stem cells for cluster annotation in single-cell analysis
single-cell
cluster-annotation
hsc
marker-gene
updated 4 days ago by
ATpoint
89k • written 2.9 years ago by
Ribo
▴ 80
0
votes
1
reply
243
views
Refcall in VCF
pass
vcf
phasing
pipeline
Refcall
4 days ago by
Mahdi&Christ
▴ 20
0
votes
1
reply
266
views
Problem with Dfam-Database and the RepeatClassifier function of repeat modeler
dfam
repeat-annotation
TE-database
repeat-masking
repeatmodeller
updated 4 days ago by
GenoMax
153k • written 4 days ago by
WaspInSpace
• 0
1
vote
1
reply
297
views
Construction of a pangenome using multiple genome sequences and read data
vg
updated 5 days ago by
colindaven
7.8k • written 5 days ago by
shcho
• 0
0
votes
0
replies
210
views
How to decide the normalization method for targeted metabolomics data ?
LC-MS
normalization
R
metabolomics
targeted-metabolomics
5 days ago by
Luwell
• 0
0
votes
1
reply
270
views
Leafcutter installation issue
Leafcutter
Conda
Devtools
updated 5 days ago by
michael.ante
★ 4.0k • written 5 days ago by
jyotik
• 0
1
vote
0
replies
228
views
How to interpret and filter vg call output VCF
graph
genotyping
pangenome
vg
VCF
5 days ago by
Tobias
▴ 40
1
vote
1
reply
412
views
Transcriptome splicing analysis tools
RNA-sequencing
splicing
updated 5 days ago by
Ram
45k • written 8 days ago by
Morris_Chair
▴ 370
0
votes
2
replies
431
views
running featureCounts on multiple bam files
RNAseq
R
updated 5 days ago by
Ram
45k • written 6 days ago by
Mamta
• 0
1
vote
3
replies
509
views
Creating sliding window for methylation data
WGBS
methylation
updated 6 days ago by
Alex Reynolds
36k • written 8 days ago by
ty.fu
• 0
0
votes
0
replies
284
views
Running time of determining graph multiplicity in unicycler
hydrid
genome
unicycler
assembly
7 days ago by
德水
• 0
0
votes
1
reply
368
views
How to get REF/ALT allele for a list of rsid and SNP notations
BED
R
Variant
VCF
SNP
updated 5 days ago by
GenoMax
153k • written 7 days ago by
Meisam
▴ 250
1
vote
7
replies
680
views
My PCA plot is weird: PC1 with 98.684% variance and PC2 with 0.582% variance
r
pca
rna-seq
visualization
updated 5 days ago by
ATpoint
89k • written 7 days ago by
undergrad_student
▴ 10
4
votes
2
replies
404
views
CTCF binding sites
genome
GENCODE
annotations
8 days ago by
pt.taklifi
▴ 70
0
votes
0
replies
306
views
News:
Workshop: Virtual RNA-seq (de novo), August 19–21
workshop
RNASeq
UConn
8 days ago by
zsc25001
▴ 10
1
vote
4
replies
490
views
Only 35 out of 800 genes in STAR reference assembly
RNAseq
transcriptomics
RNA_seq
STAR
RNA_sequencing
6 days ago by
Jasper
• 0
0
votes
0
replies
345
views
Purpose and necessity of removing PCR duplicates in m6A-seq analysis
PCR
MeRIP-seq
m6A-seq
duplicates
8 days ago by
remagen
▴ 10
0
votes
8
replies
656
views
Efficiently Converting CD-HIT-EST Clusters into .fasta Files
python
MSA
clustering
cd-hit
updated 5 days ago by
Joe
22k • written 8 days ago by
mtsrn
• 0
121,736 results • Page
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Running metaSPAdes with 71M paired-end reads: RAM and swap memory concerns
Running metaSPAdes with 71M paired-end reads: RAM and swap memory concerns
Answer: Running metaSPAdes with 71M paired-end reads: RAM and swap memory concerns
Answer: Running metaSPAdes with 71M paired-end reads: RAM and swap memory concerns
Answer: how to download gene annotation for NCBI GENE ID
Answer: how to download gene annotation for NCBI GENE ID
Comment: how to download gene annotation for NCBI GENE ID
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Recent Replies
Comment: Running metaSPAdes with 71M paired-end reads: RAM and swap memory concerns
by
Mensur Dlakic
★ 29k
It is a weekend, and I think you may want to let the computer work through it instead of you. No, it is not normal for error correction to …
Comment: Which Reference Hg38 or T2T?? Both??
by
Jon
• 0
I think I have things figured out, let me know if this makes practical sense to you. So with the Naegleria Fowleri Karachi NF001 reference,…
Comment: Running metaSPAdes with 71M paired-end reads: RAM and swap memory concerns
by
sumah.1si21bt017
▴ 20
Thank you very much, sir, for your helpful suggestions. I really appreciate your guidance. I still have a few more questions, if you don’t …
Answer: Running metaSPAdes with 71M paired-end reads: RAM and swap memory concerns
by
Mensur Dlakic
★ 29k
The answers, in the order you asked: - Most likely it will run fine, but it is generally unrealistic to expect anyone to tell you whether …
Answer: Which metric is best to represent cell-level counts/features in Seurat: raw/log-
by
ATpoint
89k
Usually for these basic QCs one uses raw counts as one wants to ensure remotely comparable sequencing depth and detected genes per cell. No…
Comment: chimeraTE GTF format error
by
frarodmar17
• 0
I checked it and it is tab-lineated. I have also removed all the rows that did not contain 9 columns. However, the error persists.
Answer: Help with bioinformatics/genetics content of my CV
by
Anchal
• 0
Hi, I'd be interested in helping. You can email your cv to me at 444aaanchal@gmail.com Best, Anchal Yadav
Comment: how to download gene annotation for NCBI GENE ID
by
GenoMax
153k
For some of the ID's included in the original question, the information in the file linked above. #tax_id GeneID Symbol LocusTag …
Answer: how to download gene annotation for NCBI GENE ID
by
Gordon Smyth
★ 8.3k
The names given in your question are already official NCBI gene symbols, as can be seen from the NCBI website: [https://www.ncbi.nlm.nih.go…
Answer: Where can I get Human microbiome dataset
by
GenoMax
153k
I assume the sample should be available in SRA. Do you know the accessions of some of the samples? If the data is available from Qiita th…
Comment: How to assess differential gene expression over gradient of treatment levels wit
by
swbarnes2
15k
If you don't expect linearity, you should do an LRT test to look for any kind of differences between any concentrations. Then you can look…
Comment: bbduk.sh trimming to BAM output file
by
Jon
• 0
HI Brian, this is off-topic a bit, but since you are the expert! I have some human blood samples that contain Naegleria Fowleri Karachi NF…
Comment: chimeraTE GTF format error
by
lieven.sterck
15k
perhaps long shot but your GTF file is tab-delineated, right? (you also did not open it in any windows/dos related software, for editing fo…
Comment: chimeraTE GTF format error
by
frarodmar17
• 0
I have just tried it but it returns the same error again
Comment: chimeraTE GTF format error
by
GenoMax
153k
Perhaps the program is only looking to get lines with `gene` attribute. You could give the following a try, which only selects lines that h…
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