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833 results • Page
4 of 17
Sort: Views
Rank
Views
Votes
Replies
1
vote
3
replies
714
views
Issues with Merging Seurat Objects: Multiple Counts in Assays Layer
Seurat
updated 14 days ago by
Felipe
• 0 • written 7 weeks ago by
dxj294
• 0
3
votes
10
replies
705
views
t-test in two groups, multiple rows
R
t-test
10 days ago by
sooni
▴ 20
6
votes
6
replies
703
views
Forum:
You have 3 days of zero obligations and expansive resources. What are you building?
hypothetical
thought-experiment
22 days ago by
jared.andrews07
★ 16k
1
vote
4
replies
697
views
gnomAD4.0 Hail Table Downloading
NGS
gnomAD
updated 14 days ago by
DBScan
▴ 300 • written 4 months ago by
adarsh_pp
▴ 40
1
vote
8
replies
683
views
6 follow
Using aspera-connect to UPLOAD fastq files to ENA on Linux
ENA
aspera-connect
ascp
updated 14 days ago by
jude
• 0 • written 15 days ago by
sue.jones
• 0
3
votes
2
replies
676
views
Seeking Beginner-Friendly Resources for Deepening Understanding of Bioinformatics Methods Post Biology Undergrad
literature
limma
updated 24 days ago by
Ram
43k • written 26 days ago by
Serij´s
• 0
0
votes
11
replies
675
views
Filtering VCF based on codon-transcript
vcf
bcftools
updated 12 days ago by
barslmn
★ 2.1k • written 23 days ago by
avelarbio46
▴ 30
0
votes
3
replies
674
views
PCR duplicates in FFPE RNASeq
PCR-duplicates
RNA-Seq
FFPE
Variant-Calling
updated 2 days ago by
Ram
43k • written 21 months ago by
Gama313
▴ 120
0
votes
1
reply
672
views
SQK-LSK112 adapter sequences
Nanopore
updated 28 days ago by
Nicolas Lichilin
▴ 20 • written 19 months ago by
zack.saud
▴ 50
4
votes
9
replies
670
views
Snakemake >= version 8 cluster configuration and SLURM job submission
parallelization
slurm
snakemake
cluster
updated 3 days ago by
Simon
▴ 10 • written 7 days ago by
Maxwell
▴ 20
3
votes
10
replies
656
views
Intersect gene IDs list and GFF3 to get the annotation.
annotation
GFF
6 days ago by
Lissa Cruz Saavedra
• 0
3
votes
12
replies
639
views
Facing problem with extracting phenotypic data from GEO
WGCNA
GEO
1 day ago by
bioinfo_enthusiast
• 0
0
votes
1
reply
635
views
Multiple replicates with one SoapDenovo-Trans run?
rna-seq
soapdenovo-trans
transcriptome
updated 29 days ago by
nargisbashir10
• 0 • written 2.3 years ago by
nina.maryn
▴ 30
3
votes
12
replies
633
views
bbmap read length from fastq
fastq
bbmap
updated 14 days ago by
GenoMax
140k • written 20 days ago by
marco.barr
▴ 30
5
votes
9
replies
627
views
Porechop output?
porechop
Nanopore
updated 27 days ago by
GenoMax
140k • written 29 days ago by
giulia.trauzzi
▴ 10
6
votes
7
replies
623
views
cutadapt not trimming all adapters in PE Illumina sequencing
NGS
Illumina
cutadapt
6 days ago by
joe
▴ 470
4
votes
10
replies
619
views
PDB residue serial inconsistency and PDB id&UniProt ID mismatch
pdb
UniProtID
pdbID
updated 28 days ago by
Wayne
★ 1.9k • written 29 days ago by
Nafi
• 0
2
votes
5
replies
607
views
I am trying to generate a bcf file through samtools mpileup but it taking too long, how long does it usually take to generate a bcf file?
alignment
sam
Bam
samtools
Bioinformatics
updated 14 days ago by
jkbonfield
★ 1.2k • written 15 days ago by
K
• 0
0
votes
2
replies
606
views
Warning: Expected at least 2 parts in FORMAT entry: ID=GP,Number=3,Type=Float,Description="Estimated Posterior Probabilities for Genotypes 0/0, 0/1 a…
vcftools
updated 19 days ago by
Pierre Lindenbaum
160k • written 19 days ago by
juan.sainz
• 0
15
votes
6
replies
599
views
Need consultation about my rna-seq workflow
RNA-seq
Gene-expression
updated 7 days ago by
Ram
43k • written 9 days ago by
markusz
▴ 10
2
votes
7
replies
598
views
Selecting query format for repeated calls to NCBI's API
NCBI
esummary
elink
API
efetch
updated 3 days ago by
GenoMax
140k • written 5 weeks ago by
LauferVA
4.1k
3
votes
5
replies
593
views
How to filter Illumina Nirvana variant annotation?
nirvana
filtration
updated 4 days ago by
Pierre Lindenbaum
160k • written 4 days ago by
Kauno tvirtovės
• 0
0
votes
6
replies
593
views
Convert Gene symbol to Ensembl ID
mygene
updated 16 days ago by
Alex Reynolds
35k • written 24 days ago by
r.shiasi3897
▴ 10
15
votes
9
replies
590
views
Forum:
F*up Night style events for Bioinformatics ? Comment if you're interested!
mistakes
updated 8 hours ago by
Dave Carlson
★ 1.7k • written 13 hours ago by
Ann
★ 2.4k
3
votes
5
replies
588
views
somatic variant calling without matched normal in long-reads
variants
cancer
illumina
ONT
nanopore
3 days ago by
eesiribloom
▴ 50
0
votes
3
replies
583
views
Calculation of λ1000 for a continuous trait
SNP
GWAS
inflation
12 days ago by
Apprentice
▴ 160
3
votes
2
replies
572
views
RNA-seq - Creating SAF from NCBI gff for Subread featureCounts - keep 'gene' or 'exon'
featureCounts
NCBI
Ensembl
GFF
rnaseq
updated 26 days ago by
Gordon Smyth
★ 6.9k • written 5 weeks ago by
BioinfGuru
★ 1.6k
3
votes
10
replies
570
views
Errors running PHG MakeInitialPHGDBPipelinePlugin (**UNASSIGNED**)
pangenome
plants
PHG
updated 14 days ago by
lcj34
▴ 410 • written 16 days ago by
b.contreras.moreira
▴ 70
0
votes
12
replies
568
views
BWA MEM different synthax on linux (bash) and macOS (zsh)
MEM
BWA
21 days ago by
gernophil
▴ 80
0
votes
2
replies
565
views
Downsampling of cells in scRNAseq DE analysis
differential
DE
expression
scRNAseq
updated 28 days ago by
fracarb8
★ 1.5k • written 11 months ago by
mytp
• 0
3
votes
4
replies
563
views
Why many organisms even though they possess mitochondrial DNA (mtDNA), it is not typically represented by chromosomes labeled as "mtDNA"?
genome
mtDNA
reference-genome
sequence
21 days ago by
George X.
• 0
8
votes
2
replies
560
views
News:
LAST CALL - Single-Cell RNA-Seq Data Analysis: A Practical Introduction (May 6-8, 2024 in Berlin)
single-cell
sequencing
22 days ago by
David Langenberger
11k
2
votes
10
replies
560
views
Can't properly use GATK Mutect2 to call somatic variants from my tumor/normal samples pair (BAM to VCF)
vaf
gatk
vcf
genomics
mutect2
updated 15 days ago by
GenoMax
140k • written 16 days ago by
Samuel
▴ 20
0
votes
2
replies
554
views
Filter out doublet and Clustering
single-cell
updated 23 days ago by
jv
★ 1.7k • written 4 months ago by
synat.keam
▴ 100
0
votes
1
reply
554
views
Downloading epigenetic and mutation data of specific TCGA BRCA samples
Mutation
RNA-Seq
TCGA
updated 10 days ago by
aUser
▴ 30 • written 2.7 years ago by
Soura
• 0
3
votes
3
replies
553
views
Whole-genome alignment visualization
cactus
maf
bigmaf
updated 28 days ago by
SanjidaR_NCBI
▴ 60 • written 5 weeks ago by
gubrins
▴ 290
1
vote
7
replies
550
views
Finding insert sequences using long reads
insert-sequences
Nanopore
long-read-assembly
updated 24 days ago by
GenoMax
140k • written 24 days ago by
bvm
▴ 20
1
vote
2
replies
545
views
Applicability of the SoupX ambient mRNA decontamination technique to fixed and/or multiplexed scRNAseq experiments
SoupX
scRNA-seq
8 days ago by
e.r.zakiev
▴ 170
1
vote
12
replies
543
views
Nanopore data filtering using fastp
fastp
nanopore
13 hours ago by
emilydolivo97
• 0
1
vote
3
replies
540
views
What is the best integration package for large single cell RNA sequencing dataset.
scRNA-seq
integration
updated 17 days ago by
rpolicastro
13k • written 9 months ago by
Andy
▴ 120
7
votes
8
replies
539
views
Forum:
Bioinformatics career transition
career
forum
updated 14 days ago by
jared.andrews07
★ 16k • written 14 days ago by
jevill17
▴ 20
8
votes
4
replies
537
views
Why employ normalization methods, and how can they be utilized in DEG analysis?
R
DEGs
normalization
17 days ago by
wyt1995
▴ 30
2
votes
2
replies
530
views
How to look up gene names using SNP locations on Practical Haplotype Graph
rphg
phg
13 days ago by
Dylan
• 0
2
votes
7
replies
525
views
Does removal of contaminants in RNAseq data have an impact on downstream analyses?
RNA-seq
contamination
updated 15 days ago by
Chris Dean
▴ 390 • written 16 days ago by
ev97
▴ 20
3
votes
7
replies
524
views
Blast NCBI online using R
R
NCBI
BLAST
Rstudio
2 days ago by
Begonia_pavonina
▴ 140
2
votes
4
replies
524
views
If the mane transcript isn't available should you use the canonical transcript?
ensembl
mane
gnomad
canonical
21 days ago by
amy__
▴ 160
2
votes
5
replies
520
views
Weird Fragment Length distribution multiQC
Salmon
RNA-seq
paired-end
MultiQC
updated 17 days ago by
GenoMax
140k • written 28 days ago by
_deb
• 0
3
votes
6
replies
520
views
Target deletions with adaptive sampling
microdeletions
nanopore
AdaptiveSampling
16 days ago by
njornet
▴ 10
5
votes
4
replies
519
views
Separation of haplotypes in genome assembly
Haplotypes
pacbio
assembly
genome
reads
27 days ago by
sansan_96
▴ 50
9
votes
7
replies
518
views
Getting fasta file from the VCF after variant calling
fastq
pangolin
assembly
updated 19 days ago by
Michael
54k • written 21 days ago by
Neil
▴ 20
833 results • Page
4 of 17
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Answer: log2(TPM+1)
Comment: Error in openning FastQC
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
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Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Yikes. Well, this is from an Illumina MiniSeq. Sure, I will use alignment, but only to remove host reads. Then the remaining reads will go …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
This is going to be tough to diagnose. Are you going to align to a reference? If so go ahead with the alignments to see if alignments turn …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Thank you for replying. I have separated the reads with at least one N on them and they account for 0.2% of the total reads in the file (8'…
Comment: Error running local blastn in R using system2
by
Mensur Dlakic
★ 26k
The `-db data/nt_euk` switch means that in your current directory you have a subdirectory called `data`, and all the `nt_euk` files are in …
Comment: Low number of both surviving reads after trimming
by
Jay
• 0
Thank you for your opinion. I will try with lower LEADING and TRAILING bases. By the way, I tried to set `keepBothReads:true` through sear…
Comment: Error in openning FastQC
by
GenoMax
140k
At this point it would be beneficial to learn some of the basics of command line. Please use this UNIX tutorial since you seem to be new to…
Comment: vcf file: number of samples does not match number of columns
by
Pierre Lindenbaum
160k
> ore or have any suggestions for fixing it? it's a problem with your upstream process. You'd better fix it.
Comment: Error in openning FastQC
by
friszd
• 0
after running fastqc -o output.html input.fastq, terminal returns: " Specified output directory 'output.html' does not exist " , when i run…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
The question you should be looking into is why the Q scores are dropping there? Are there `N` calls indicating some issue with that cycle?
Comment: Error in openning FastQC
by
GenoMax
140k
What is `ctrl+c ctrl+v`? You may actually be killing the running fastqc process. If you run `fastqc` interactively (like what was shown ab…
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Dave Carlson
★ 1.7k
Ugh. I've definitely done this one before as well. And was none too happy about it.
Comment: Error in openning FastQC
by
friszd
• 0
fastqc -o output.html input.fastq ctrl+c ctrl+v
Comment: Error running local blastn in R using system2
by
GenoMax
140k
What do you see if you `cat nt_euk.nal`? Do the number of pieces mentioned in that file match with what you locally have?
Comment: Low number of both surviving reads after trimming
by
GenoMax
140k
It is your data and if you want to do that it is up to you. You may be throwing away essentially good data (you should remove the nextera s…
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Istvan Albert
100k
Some things never change ... the most common mistake is still the one on top there
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