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122,202 results • Page
687 of 2445
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
882
views
Plot only the genome-wide trans contacts in a Hi-C matrix (no cis contacts)
juicer
Hi-C
inter-chromosomal
cooler
trans
4.7 years ago by
kalavattam
▴ 380
1
vote
10
replies
2.5k
views
How to remove these a subset fasta file
orfipy
updated 4.6 years ago by
Ram
45k • written 4.7 years ago by
CHINMAYA
▴ 10
7
votes
7
replies
26k
views
Calculating fpkm from raw counts
RNA-Seq
R
fpkm
updated 4.2 years ago by
TheVavish
▴ 10 • written 7.6 years ago by
vinayjrao
▴ 260
0
votes
2
replies
2.3k
views
How to calculate frequency of heterozygous SNPs in multisample VCF file and to filter out over a specific range?
bcftools
vcftools
4.6 years ago by
kumar.vinod81
▴ 340
3
votes
7
replies
3.0k
views
How to add gene function/protein name, start and end position to DESeq2 results for bacteria
deseq2
annotation
updated 4.7 years ago by
Michael
56k • written 4.7 years ago by
Miguel
• 0
1
vote
0
replies
1.9k
views
Job:
Software Developer: EB-Environ Genomics & Systems Bio
JSON-Schema
LinkML
Python
UML
updated 2.7 years ago by
Ram
45k • written 4.7 years ago by
BerkeleyLab
▴ 70
4
votes
2
replies
4.5k
views
Trouble downloading files with fasterq-dump
sratoolkit
4.7 years ago by
Rogerio Ribeiro
▴ 110
0
votes
0
replies
2.3k
views
Job:
Postdoc position in microbiome gut-brain neuroscience @ Singapore A*STAR NTU ; 新加坡科技研究局南洋理工大学医学院诚聘博士后
neuroscience
behavior
microbiome
updated 4.4 years ago by
Ram
45k • written 4.7 years ago by
Singapore Research
• 0
0
votes
0
replies
723
views
using RNAseq reads to verify predicted gene models
prediction
gene
RNA-seq
4.7 years ago by
sullis02
▴ 40
3
votes
3
replies
2.2k
views
Simulate 100 Reads from .fastq file | FASTQC
fastq
FASTQC
Linux
updated 20 months ago by
Ram
45k • written 4.7 years ago by
Anonymous
▴ 10
1
vote
2
replies
1.4k
views
CDS regions of a gene
coding
regions
CDS
two
sequences
FASTA
4.7 years ago by
ali.al-fatlawi
▴ 10
3
votes
7
replies
5.6k
views
bash: sudo: command not found | ea-utils installation [CLOSED]
fastq
ea-utils
reads
bash
linux
4.7 years ago by
Anonymous
▴ 10
0
votes
0
replies
999
views
Parsing a bed file to vcf file in Python
python3.8
python
4.7 years ago by
alex_gon87
• 0
0
votes
0
replies
707
views
Hosting scRNA-seq data for query
Shiny
Seurat
scRNA-seq
4.7 years ago by
LacquerHed
▴ 30
0
votes
0
replies
829
views
Comparison of ChIP-seq tracks from two cell lines using FC over control (ENCODE data)
ChIP-seq
H3K27ac
bigWig
ENCODE
4.7 years ago by
erica.fary
▴ 20
9
votes
9
replies
4.7k
views
Where can I lookup old merged rsIDs?
SNP
updated 4.7 years ago by
Vince Carey
▴ 80 • written 8.8 years ago by
Mike Dacre
▴ 150
0
votes
1
reply
1.0k
views
BlastN - Optimal recipocal blast command line options ?
alignment
blastn
updated 4.7 years ago by
lieven.sterck
16k • written 4.7 years ago by
sunnykevin97
▴ 1000
3
votes
4
replies
2.8k
views
bash: conda: command not found | for SimLord [CLOSED]
windows
bash
simlord
miniconda
updated 4.7 years ago by
GenoMax
154k • written 4.7 years ago by
Anonymous
▴ 10
0
votes
11
replies
7.8k
views
Extracting reads from one barcode in a bam file
extract
bam
barcode
4.6 years ago by
msrinivasan
• 0
0
votes
1
reply
1.1k
views
How to make factor level dynamic input field in shiny dashboard
flexdashboard
shinydashboard
shiny
updated 4.7 years ago by
Kevin Blighe
★ 90k • written 4.7 years ago by
majeedmj.ict
▴ 20
1
vote
5
replies
6.6k
views
Multiple Psi-Blast Iterations From Command Line Using Remote Database
blast
pssm
updated 4.5 years ago by
nataliagru1
▴ 90 • written 12.9 years ago by
jdromano2
▴ 10
1
vote
6
replies
3.6k
views
Dealing with chimeric assembly contigs
comperative-genomics
assembly
chimera-contig
updated 4.6 years ago by
samuel.a.odonnell
▴ 640 • written 4.7 years ago by
langziv
▴ 70
0
votes
0
replies
1.0k
views
Nucleotide diversity obtained from Arlequin
Haplotype
Nucleotide
Arlequin
DnaSP
diversity
4.7 years ago by
apl00028
▴ 90
5
votes
8
replies
3.0k
views
What are the necessary and sufficient conditions for applying a multiple hypothesis correction?
multiple-comparisons
statistics
updated 4.6 years ago by
Jeremy Leipzig
23k • written 4.7 years ago by
Aspire
▴ 390
2
votes
2
replies
2.0k
views
Different Sequence Length Distribution between forward and reverse reads
FastQC
Length
Distribution
human
DNA
Sequence
4.6 years ago by
Linda
• 0
2
votes
4
replies
2.6k
views
ATAC-seq - remove mt reads using KMC
samtools
chrM
ATAC-seq
mitochondria
KMC
4.7 years ago by
maxrwjones
▴ 60
0
votes
1
reply
1.5k
views
STRINGdb r package blocked by antivirus and changes output?
STRINGdb
R
updated 4.6 years ago by
Kevin Blighe
★ 90k • written 4.7 years ago by
DN99
▴ 20
0
votes
0
replies
1.4k
views
Which Manta output file one must consider in a joint tumor/normal SVs call?
Structural
Variants
Manta
4.7 years ago by
giusdalt95
▴ 10
0
votes
0
replies
1.4k
views
SEACR multiple control files
IgG
peak-calling
SEACR
CutAndRun
updated 2.1 years ago by
Ram
45k • written 4.7 years ago by
a_bis
▴ 40
1
vote
1
reply
839
views
Compare different microbial databases
comparison
microbial
databases
updated 4.7 years ago by
GenoMax
154k • written 4.7 years ago by
Molinia
▴ 10
1
vote
2
replies
3.0k
views
Most stringent settings for bwa mem
alignment
bwa
dna
updated 4.7 years ago by
Istvan Albert
103k • written 4.7 years ago by
nanana
▴ 120
1
vote
2
replies
1.4k
views
How to interpret De Novo Sequence from Trinity
novo
trinity
de
4.7 years ago by
progistar
▴ 40
0
votes
0
replies
814
views
IVA: kmc error
shiver
genomeassembly
hiv
4.7 years ago by
waqasnayab
▴ 250
1
vote
1
reply
1.3k
views
Cystoscope network visualization
STRING
Ctopscape
updated 4.7 years ago by
tothepoint
▴ 940 • written 4.7 years ago by
1961012
▴ 20
0
votes
2
replies
1.5k
views
so any method to remove header part of FASTA file
fasta
updated 4.7 years ago by
finswimmer
16k • written 4.7 years ago by
CHINMAYA
▴ 10
2
votes
4
replies
1.7k
views
What are the disadvantages of increasing the sequencing depth of RNA-seq experiment?
NGS
RNA-Seq
sequencing
depth
transcriptome
4.7 years ago by
mrj
▴ 180
0
votes
0
replies
1.1k
views
Missing Kraken database.kdb file
kraken
4.7 years ago by
valentinav
• 0
1
vote
3
replies
2.3k
views
Searching for conserved domains in a chromosome/scaffold
blast
domain
CDD
PSSM
rpsblast
updated 4.7 years ago by
Mensur Dlakic
★ 30k • written 4.7 years ago by
rubic
▴ 270
1
vote
6
replies
2.9k
views
How to add space in specific location in a barplot using ggplot2
GROUPING
R
GGPLOT2
updated 4.6 years ago by
Ram
45k • written 4.7 years ago by
diqixiaoyaoer
▴ 20
0
votes
0
replies
769
views
SortmeRNA error
SortmeRNA
RNA-seq
updated 4.7 years ago by
GenoMax
154k • written 4.7 years ago by
pallob.barai
• 0
0
votes
5
replies
2.3k
views
How to use the goseq for ensemble gene ID
RNA-SEQ
R
annotations
GO
4.7 years ago by
BISEP
▴ 10
0
votes
1
reply
1.3k
views
Are ribosomal protein coding genes depleted as well during rRNA depletion?
rRNA
RNA-seq
depletion
annotations
updated 4.7 years ago by
GenoMax
154k • written 4.7 years ago by
akibio
• 0
0
votes
0
replies
804
views
How to calculate power to detect mQTLs?
Illumina
power
mqtl
methylation
4.7 years ago by
anamaria
▴ 220
0
votes
1
reply
1.8k
views
merging fastq paired ends
Illumina
fastq
seqtk
updated 4.7 years ago by
GenoMax
154k • written 4.7 years ago by
HT
• 0
0
votes
1
reply
1.5k
views
Bioinformatics definition of TAD boundary
hiTADs
Hi-C
TAD
updated 4.5 years ago by
kalavattam
▴ 380 • written 4.7 years ago by
sckinta
▴ 740
1
vote
2
replies
1.1k
views
miRNA length distribution
miRNA
rna
small
4.7 years ago by
LynxLynx
• 0
0
votes
1
reply
770
views
Python/Perl/R to export Nucleotide/Amino Acid Sequence of Genomic Variants
gene
genomics
analysis
updated 4.4 years ago by
Ram
45k • written 4.7 years ago by
Rookie
• 0
1
vote
0
replies
6.2k
views
Seurat FindVariableFeatures algorithm understanding Single Cell
Seurat
algorithm
selection
feature
4.7 years ago by
Matt
▴ 20
0
votes
2
replies
1.2k
views
Power analysis to determine sample size for a single-cell sequencing study
sequencing
single-cell
4.7 years ago by
halo22
▴ 300
0
votes
1
reply
1.8k
views
fastq-dump and fasterq-dump not working
fastq
prefetch
ncbi
sratoolkit
updated 4.4 years ago by
Ram
45k • written 4.7 years ago by
HaroonPakistan
• 0
122,202 results • Page
687 of 2445
Recent Votes
what cause poly-G from NextSeq
what cause poly-G from NextSeq
A: what cause poly-G from NextSeq
A: what cause poly-G from NextSeq
How to trim transcripts using information from NCBI contamination screen report
How to trim transcripts using information from NCBI contamination screen report
Trimming sequences based on NCBI contamination screen report
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Recent Replies
Answer: Chip-seq analysis Diffbind
by
ATpoint
90k
I think the results are expected. a) n=2 is underpowered, for any assay and in particular for ChIP-seq which has considerable noise. b) you…
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Wu-Sheng Zhang
▴ 10
Hi @arup , after changing the file name following the read length, I can process them using cellranger arc successfully. Thank you very muc…
Comment: Visualize methylation status in Pacbio Hifi read
by
cmdcolin
★ 4.4k
(as the JBrowse dev) I'm glad to hear this. if you see any trouble with it feel free to let me know, I have tried to keep up to date with m…
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Wu-Sheng Zhang
▴ 10
Got it! I will try to switch their name and re-run the cellranger arc. Thank you very much, @arup !
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Arup Ghosh
3.5k
The barcode files with 24nt read length W71_LUNGrep2_S6_L001_R3_001.fastq.gz and W71_LUNGrep2_S6_L002_R3_001.fastq.gz should be the R2.
Comment: ID unifiying across different datasets
by
GenoMax
154k
Each database has their own method of annotation/validation. Depending on resources available there may be a lag between the databases in t…
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Wu-Sheng Zhang
▴ 10
Hi @arup , thank you very much for your suggestions, and here are the results -- they seems correct. May I have your suggestions? Thank you…
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding
by
samuel.a.odonnell
▴ 640
I don't believe merqury ignores softmasked (lower case) nucleotides so I don't think that is the case. From what it sounds like, during th…
Comment: ID unifiying across different datasets
by
zizigolu
★ 4.4k
Thanks a lot to be helpful I’m trying to build a complete `UniProtID` to `GeneSymbol` lookup table and I’m running into a wall. I’ve alrea…
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria
by
thomas.heigl.ibk
▴ 20
thanks for the quick reply. i posted the screenshot. gatk-internally, there is still the difference using -ERC or not, priot is getting …
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria
by
thomas.heigl.ibk
▴ 20
here the igv view. showing the histogram for all samples plus the reads for one: ![enter image description here][1] and expanded view of …
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Arup Ghosh
3.5k
Check the read lengths to make sure the files are correct.
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria
by
Pierre Lindenbaum
166k
> Any suggestions or help you could share please, show us an IGV screenshot of the position GATK realign the reads locally, discards read…
Comment: Can i use orthofinder for small protein datasets and not full proteome?
by
alexandrakortsi
• 0
By sequence. Thank you for your response!
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding
by
xinguok794
▴ 10
Thank you for your reply! Unfortunately, despite running YAHS with `--no-contig-ec`, the QV value of the resulting FASTA file did not impro…
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