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231 results • Page
2 of 5
Sort: Views
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Views
Votes
Replies
0
votes
0
replies
843
views
Variant quality scores with different variant caller: HaplotypeCaller vs DeepVariant. How to interpret the quality scores?
variant-calling
DeepVariant
HaplotypeCaller
quality-score
updated 3 days ago by
Ram
43k • written 2.4 years ago by
Jordi
▴ 50
1
vote
7
replies
831
views
GATK Mutect2 Input files reference and features have incompatible contigs: No overlapping contigs found.
hg19
Mutect2
GATK
Variant-Calling
updated 3 days ago by
Ram
43k • written 8 months ago by
Manuel Sokolov Ravasqueira
▴ 100
2
votes
11
replies
805
views
RNA seq aligner?
Alignment
4 days ago by
tesfaye
• 0
0
votes
12
replies
776
views
What is the sequence origin in human plasma?
human
sequence
cfDNA
3 days ago by
biwdpang
• 0
0
votes
1
reply
750
views
Error in genetics vcf file - !! Error (genfile::MalformedInputError): Source "file-path/data_chrxx.vcf.gz" is malformed on line 5145934..
vcf
genetics
updated 4 days ago by
m.medinagomez
• 0 • written 2.3 years ago by
Nance
• 0
1
vote
3
replies
747
views
Can shotgun metagenome approaches effectively target both RNA and DNA viruses in low-viral-load water samples?
RNA-virus
binning
metagenome
abundance
shotgun
updated 5 days ago by
joe
▴ 470 • written 7 days ago by
mathavanbioinfo
▴ 80
2
votes
10
replies
730
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 1 day ago by
Ram
43k • written 5 weeks ago by
Sky
▴ 10
0
votes
3
replies
674
views
PCR duplicates in FFPE RNASeq
PCR-duplicates
RNA-Seq
FFPE
Variant-Calling
updated 3 days ago by
Ram
43k • written 21 months ago by
Gama313
▴ 120
4
votes
9
replies
671
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
16
votes
10
replies
663
views
6 follow
Forum:
F*up Night style events for Bioinformatics ? Comment if you're interested!
mistakes
updated 1 hour ago by
Madelaine Gogol
5.3k • written 22 hours ago by
Ann
★ 2.4k
3
votes
10
replies
657
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
644
views
Facing problem with extracting phenotypic data from GEO
WGCNA
GEO
2 days ago by
bioinfo_enthusiast
• 0
6
votes
7
replies
623
views
cutadapt not trimming all adapters in PE Illumina sequencing
NGS
Illumina
cutadapt
6 days ago by
joe
▴ 470
2
votes
7
replies
599
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 5 days ago by
Pierre Lindenbaum
160k • written 5 days ago by
Kauno tvirtovės
• 0
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
1
vote
12
replies
550
views
Nanopore data filtering using fastp
fastp
nanopore
23 hours ago by
emilydolivo97
• 0
3
votes
7
replies
525
views
Blast NCBI online using R
R
NCBI
BLAST
Rstudio
2 days ago by
Begonia_pavonina
▴ 140
2
votes
3
replies
512
views
Website or tool to obtain a list of genes that participate in a specific process?
genomics
updated 1 day ago by
NancyTLi
• 0 • written 3 months ago by
Hamtaro
▴ 50
0
votes
1
reply
496
views
Which fasta files are assembled transcripts IDBA_tran assembler ?
RNA-Seq
Assembly
updated 1 day ago by
weidonglu
• 0 • written 3.8 years ago by
sunnykevin97
▴ 980
6
votes
13
replies
487
views
Allocating right resources to HPC using LSF scheduler
BWA
GATK
hpc
lsf
bsub
3 days ago by
Maverick
▴ 10
0
votes
1
reply
485
views
Nanopore multisample variant calling
SNPs
nanopore
SNP-calling
variants
multisample
updated 4 hours ago by
emilydolivo97
• 0 • written 2.1 years ago by
colindaven
6.3k
2
votes
3
replies
479
views
Should I use Dfam or a custom repetitve elements library (from PlantRep) as a repeat database; using RepeatMasker in a Linux machine?
genome
sequence
repeatmasker
blast
updated 2 days ago by
b.contreras.moreira
▴ 70 • written 3 days ago by
Vijith
▴ 30
1
vote
1
reply
476
views
Help with SCENIC+
scenic-plus
updated 5 days ago by
corbettberry
▴ 10 • written 5 months ago by
Chris
▴ 260
0
votes
1
reply
474
views
Tool:
tinybio added sources & chat history - (ChatGPT optimized for bioinformatics questions)
gpt
updated 5 days ago by
Shaunak
• 0 • written 9 months ago by
Sasha
▴ 830
0
votes
9
replies
462
views
Nextflow ERROR : Timeout waiting for connection from pool
nextflow
updated 1 day ago by
GenoMax
140k • written 7 days ago by
dzisis1986
▴ 70
1
vote
6
replies
461
views
Quest about the input data for PCA analysis
PCA
6 days ago by
tujuchuanli
▴ 100
0
votes
5
replies
456
views
How to download RNAseq data of only male KIRC patients?
TCGAbiolinks
3 days ago by
bioinfo_enthusiast
• 0
2
votes
5
replies
453
views
Searching for gene in multiple genomes
gene
genome
alignment
sequence
updated 6 days ago by
BioinfGuru
★ 1.6k • written 7 days ago by
Miya
• 0
2
votes
6
replies
453
views
Need help understanding core SNPs
SNPs
snippy
4 days ago by
ujichu
• 0
3
votes
13
replies
445
views
Variant calling of GBS data
GBS
variants
BQSR
21 hours ago by
analyst
▴ 10
0
votes
8
replies
420
views
STAR aligner options
STAR
1 day ago by
theophile
• 0
8
votes
6
replies
409
views
Pangenome of plant
pangenome
plant
updated 1 day ago by
talbots
• 0 • written 2 days ago by
analyst
▴ 10
0
votes
5
replies
409
views
Deeptools scale issue for plotHeatmap
deeptools
computeMatrix
plotHeatmap
6 days ago by
Learner
• 0
0
votes
1
reply
405
views
Get_Homologues
get_homologues
homologues
clusters
updated 2 days ago by
b.contreras.moreira
▴ 70 • written 5 months ago by
utkarsh.sood
▴ 40
3
votes
5
replies
381
views
Losing my mind with a VCF problem
vcf
bcftools
updated 6 days ago by
Michael
54k • written 6 days ago by
a.beggs
▴ 30
1
vote
6
replies
372
views
Coverage depth map of genome from multiple sample coverage bedgraphs?
bedops
bedmap
coverage
3 days ago by
Agastya
▴ 10
0
votes
3
replies
364
views
FindAllMarkers not working (Error (data layers are not joined. Please run JoinLayersWarning: When testing 1 versus all)
FindAllMarkers
seurat
re-clustering
23 hours ago by
Nitin
• 0
0
votes
0
replies
362
views
SNV occuring 2 fold more in forward than in reverse reads should be filtered?
Variant-Calling
updated 3 days ago by
Ram
43k • written 2.2 years ago by
jeni
▴ 90
2
votes
4
replies
354
views
Visualizing human genomic loci
Genome
visualization
3 days ago by
James
▴ 10
1
vote
2
replies
348
views
How to extract unmapped reads to assemble a plasmid
plasmid
transconjugant
reference-genome
5 days ago by
Barbara
• 0
1
vote
2
replies
345
views
What is meant by 'genomic order' in gatk's GatherVcfs, and how do I check for it?
gatk
vcf
merge
updated 5 days ago by
Pierre Lindenbaum
160k • written 5 days ago by
8armed
• 0
1
vote
8
replies
342
views
0-based coordinates from samtools depth
samtools
coverage
depth
updated 4 days ago by
Pierre Lindenbaum
160k • written 4 days ago by
marco.barr
▴ 30
2
votes
4
replies
338
views
Hybrid assembly Pacbio- Nanopore
long-reads
hybric
assembly
genome
short-reads
21 hours ago by
Lissa Cruz Saavedra
• 0
0
votes
0
replies
336
views
Benchmarking pipeline for Variant identification using RNA-seq data
RNA-seq
somatic
Variant-calling
germline
updated 3 days ago by
Ram
43k • written 17 months ago by
ahkam.s
• 0
1
vote
3
replies
326
views
Combining and Forward and Reverse Reads
genome
alignment
concatenation
sequencing
4 days ago by
SineWave
• 0
5
votes
2
replies
325
views
Forum:
Can questions and answers on biostars be asked only in English? Can't I use Russian for example?
language
updated 4 days ago by
Michael
54k • written 4 days ago by
avpuzanov
• 0
0
votes
7
replies
324
views
Salmon Quantification in Alignment based-mode
Salmon
RNA-seq
TPM
updated 1 day ago by
GenoMax
140k • written 2 days ago by
Patadu94
• 0
0
votes
5
replies
317
views
Parsing fasta file by coordinates
linux
fasta
updated 21 hours ago by
GenoMax
140k • written 3 days ago by
sorrymouse
▴ 120
1
vote
11
replies
316
views
struggle to get fasta files from ucsc goldenPath
ucsc
getfasta
fasta
updated 21 hours ago by
GenoMax
140k • written 1 day ago by
Lila M
★ 1.2k
231 results • Page
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Synthetic lethality and cancer database
Answer: log2(TPM+1)
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Comment: Error running local blastn in R using system2
by
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• 0
Yes, in my actual script I use the whole path to nt_euk. I was just showing `C:/data/nt_euk` as shorthand for the full path. There are no s…
Comment: Error running local blastn in R using system2
by
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by
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140k
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140k
You will have to use a programming approach. BioPython is one option: https://warwick.ac.uk/fac/sci/moac/people/students/peter_cock/python/…
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That sounds fun, and I've got some of these that I have told many people about (to keep them from making the same mistakes as me). I am pla…
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for hgnc and ensembl that can be done for transcript id for human to mouse ortholog its difficult to parse and map the exact version from g…
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That error is on the server side, nothing to do with you, and is very common. Usually the fix is to try again in an hour, or to insert host…
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by
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• 0
hello @colindaven , Did you find a suitable tool for this purpose please ? I'm dealing with fungal dataset
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Can you upload or post a link to the genbank file please?
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It's the case that there's no indication of multi-threading in the documentation. However, it made me wonder why the developers would restr…
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