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238 results • Page
2 of 5
Sort: Votes
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Views
Votes
Replies
2
votes
10
replies
728
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 19 hours ago by
Ram
43k • written 5 weeks ago by
Sky
▴ 10
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
2
votes
11
replies
805
views
RNA seq aligner?
Alignment
4 days ago by
tesfaye
• 0
2
votes
2
replies
229
views
singlecell annotation
scRNA-seq
annotation
2 days ago by
kayah
• 0
2
votes
2
replies
216
views
A pipeline for prediction and annotation of obelisks
rna-seq
updated 1 day ago by
Pierre Lindenbaum
160k • written 2 days ago by
fred.s.kremer
▴ 110
2
votes
5
replies
1.8k
views
alignement and Variant calling with BWA and samtools
variant-calling
samtools
BWA
updated 2 days ago by
Ram
43k • written 2.9 years ago by
simon.burgermeister
▴ 30
2
votes
3
replies
213
views
Reference mouse phased vcf
mm10
vcf
phasing
Beagle
4 days ago by
machoo
• 0
2
votes
3
replies
478
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 1 day ago by
b.contreras.moreira
▴ 70 • written 2 days ago by
Vijith
▴ 30
2
votes
1
reply
301
views
Tool:
TGSFilter, An ultra-fast and efficient tool for long reads filtering and trimming
genome-assembly
filtering
reads
trimming
updated 4 days ago by
Yingzi
• 0 • written 5 days ago by
Huiyang
▴ 180
2
votes
4
replies
352
views
Visualizing human genomic loci
Genome
visualization
3 days ago by
James
▴ 10
2
votes
1
reply
301
views
GIS overlay for environmental samples from NCBI
NCBI
environmental
SRA
GIS
ArcPro
6 days ago by
joe
▴ 470
2
votes
6
replies
3.3k
views
Base Quality of a reported variant in VCF
alignment
FASTQ
VCF
next-gen
Variant-Calling
updated 2 days ago by
Ram
43k • written 9.1 years ago by
VineethVenumadhavan
▴ 50
2
votes
3
replies
242
views
Extracting information from my VCF file
VCF
updated 2 days ago by
bioruffo
▴ 40 • written 2 days ago by
realtreeecat
• 0
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
2
votes
2
replies
203
views
Location of NCBI ftp site changed?
ftp
ncbi
2 days ago by
sampsa.hyvamaki
• 0
2
votes
5
replies
976
views
Why multiple SYMBOLS, Consequences... for Variant Effect Predictor (VEP)
VEP
updated 2 days ago by
barslmn
★ 2.1k • written 15 months ago by
gernophil
▴ 80
2
votes
1
reply
1.1k
views
Using the ranking value to filter
discosnp
RNA-Seq
variant-calling
updated 2 days ago by
Ram
43k • written 6.0 years ago by
vguerracanedo
▴ 10
2
votes
2
replies
222
views
Infering the cell composition from bulk RNA-seq data for mouse
RNA-seq
deconvolution
mouse
6 days ago by
feather-W
• 0
2
votes
5
replies
452
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
4
replies
328
views
Hybrid assembly Pacbio- Nanopore
long-reads
hybric
assembly
genome
short-reads
15 hours ago by
Lissa Cruz Saavedra
• 0
2
votes
6
replies
453
views
Need help understanding core SNPs
SNPs
snippy
3 days ago by
ujichu
• 0
1
vote
2
replies
234
views
Kmers unique mapping
KMC
alignment
bowtie
kmers
6 days ago by
enee
▴ 10
1
vote
1
reply
170
views
Forum:
Can I use this community for software development?
software-development
updated 3 days ago by
Ram
43k • written 4 days ago by
avpuzanov
• 0
1
vote
12
replies
547
views
Nanopore data filtering using fastp
fastp
nanopore
18 hours ago by
emilydolivo97
• 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
1
vote
3
replies
2.0k
views
psmc bootstrapping help
bootstrap
psmc
updated 3 days ago by
xuby963
• 0 • written 3.1 years ago by
truebeliever24
▴ 50
1
vote
1
reply
475
views
Help with SCENIC+
scenic-plus
updated 5 days ago by
corbettberry
▴ 10 • written 5 months ago by
Chris
▴ 260
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
0
replies
97
views
Downloading immne signature and pathway signature genes form publication and KEGG
genes
TRANSCRIPTOME_signature
3 days ago by
mrazib0210
▴ 10
1
vote
5
replies
444
views
Not getting any modification calls in nanopore reads with dorado basecaller
mofications
dorado
basecalling
nanopore
methylation
updated 6 days ago by
LauferVA
4.1k • written 7 days ago by
njornet
▴ 10
1
vote
8
replies
342
views
0-based coordinates from samtools depth
samtools
coverage
depth
updated 3 days ago by
Pierre Lindenbaum
160k • written 3 days ago by
marco.barr
▴ 30
1
vote
2
replies
347
views
How to extract unmapped reads to assemble a plasmid
plasmid
transconjugant
reference-genome
5 days ago by
Barbara
• 0
1
vote
1
reply
290
views
diffbind : killed dba.count(DBsample, bParallel=FALSE)
diffbind
r
atacseq
21 hours ago by
Pierre Lindenbaum
160k
1
vote
0
replies
109
views
checkm lineage.ms output file
checkm
lineage
4 days ago by
A_heath
▴ 160
1
vote
1
reply
196
views
genome.fa to indix files to use it in rna-seq analysis
RNA-seq
hisat2
index
updated 6 days ago by
GenoMax
140k • written 6 days ago by
Hasan_Daaboul
• 0
1
vote
3
replies
1.2k
views
esearch get taxonomy ID from a large list of accession IDs
esearch
ubuntu
updated 1 day ago by
Bertalan_Takacs
▴ 90 • written 20 months ago by
garfield320
▴ 20
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 2 days ago by
Ram
43k • written 8 months ago by
Manuel Sokolov Ravasqueira
▴ 100
1
vote
2
replies
929
views
How to display gene expression after Harmony correction in scRNA-seq analysis
scRNA-seq
correction
Harmony
6 days ago by
tujuchuanli
▴ 100
1
vote
6
replies
461
views
Quest about the input data for PCA analysis
PCA
6 days ago by
tujuchuanli
▴ 100
1
vote
2
replies
223
views
Is it possible to see so little adipocyte in white adipose tissue?
scRNA-seq
2 days ago by
kayah
• 0
1
vote
1
reply
154
views
Pool-Seq same as normal variant calling?
Pool-Seq
Variant-Calling
updated 2 days ago by
dthorbur
★ 1.7k • written 2 days ago by
andrebolerbarros
• 0
1
vote
2
replies
918
views
Jupyter notebook installation
Jupyter
updated 2 days ago by
chictu
▴ 10 • written 7 months ago by
sarahmanderni
▴ 100
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
1
vote
0
replies
100
views
Job:
Job Opening - Fred Hutch - Director of Training & Community
fred-hutchinson
updated 2 days ago by
Ram
43k • written 3 days ago by
Fred Hutch (Recruiting)
▴ 20
1
vote
2
replies
188
views
vg call is time consuming
vg
1 day ago by
Maxine
▴ 40
1
vote
3
replies
326
views
Combining and Forward and Reverse Reads
genome
alignment
concatenation
sequencing
4 days ago by
SineWave
• 0
1
vote
2
replies
233
views
BWA MEM Alignment mapped small part of the reads!!
bwa
mem
updated 2 days ago by
bioruffo
▴ 40 • written 3 days ago by
Bunit
• 0
1
vote
6
replies
2.4k
views
Variant calling from multiple sequencing runs for a single samples
variant-calling
updated 2 days ago by
Ram
43k • written 6.9 years ago by
harish.nucl
• 0
1
vote
1
reply
1.8k
views
Intronic Variant Filtering
variant-calling
snp
updated 2 days ago by
Ram
43k • written 6.7 years ago by
cvu
▴ 180
1
vote
13
replies
967
views
error when running phg create-maf-vcf to build a built practical haplotype graph (v2)
pangenome
phg_v2
plants
PHG
updated 3 days ago by
lcj34
▴ 410 • written 9 days ago by
b.contreras.moreira
▴ 70
238 results • Page
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Recent Votes
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Synthetic lethality and cancer database
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I usually perform biomaRt queries with their `getBM()` function where I list the input using `filter` and `values` option and my request in…
Comment: DESeq2 and normalization
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Thank you for your response. I have often seen commands like dds <- estimateSizeFactors(dds) normalized_counts <- counts(dds, normalized=T…
Comment: Number of CPUs to use by DRAP for transcriptomic assmbly
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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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Bulk RNAseq from any sample is still considered a bulk sample. Running bulk RNA sequencing on a sample with any level of cell type/state c…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
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Comment: Is it reasonable to discard reads that show variation of quality across its leng
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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'…
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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
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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…
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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…
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> ore or have any suggestions for fixing it? it's a problem with your upstream process. You'd better fix it.
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after running fastqc -o output.html input.fastq, terminal returns: " Specified output directory 'output.html' does not exist " , when i run…
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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?
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Dave Carlson
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Ugh. I've definitely done this one before as well. And was none too happy about it.
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