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122,217 results • Page
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Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
862
views
LOH Score or rate
ngs
wxs
next-gen
snp
4.8 years ago by
biom.andressa
▴ 10
0
votes
1
reply
729
views
?Trimming advice with separate ChIP-seq experiments
ChIP-Seq
Trimming
4.8 years ago by
drodavis0
• 0
0
votes
0
replies
792
views
Structural variants call from circular genome
Assembly
structural variants
bacterial genome
4.8 years ago by
rthapa
▴ 90
21
votes
9
replies
9.2k
views
7 follow
bioawk installation issue "command not found"
bioawk
updated 3.2 years ago by
Ram
45k • written 10.2 years ago by
aremkho
▴ 10
1
vote
3
replies
1.2k
views
supernova 10X assembler
Assembly
supernova10x
4.8 years ago by
oussama.badad
▴ 10
0
votes
3
replies
1.2k
views
Supplementary aligments in VAF
alignment
sequencing
genome
snp
frequency
4.8 years ago by
deniselavezzari
• 0
0
votes
6
replies
2.0k
views
How to extract all gene nucleotide sequences separately from multiple Genbank files, with the form ">gene_name organism_name?
sequence
alignment
4.8 years ago by
jbt38
• 0
1
vote
3
replies
1.6k
views
Best Practices for chi-seq analysis
ChIP-Seq
updated 4.8 years ago by
predeus
★ 2.1k • written 4.8 years ago by
luckysardar171
▴ 20
2
votes
4
replies
1.7k
views
File convert vcf to .bed format with plink2
SNP
vcf
ddRAD
updated 4.8 years ago by
Ram
45k • written 4.8 years ago by
safiq713
▴ 10
58
votes
43
replies
21k
views
8 follow
Forum:
Best RNA-Seq aligner: A comparison of mapping tools
NGS
alignment
genome
RNA-Seq
sequence
updated 2.7 years ago by
Ram
45k • written 6.9 years ago by
David Langenberger
11k
0
votes
0
replies
724
views
Patient-to-patient similarities network
SNFtools
multi omics
4.8 years ago by
Omics data mining
▴ 260
0
votes
6
replies
1.6k
views
Merging paired fastq read files with small overlap region.
sequencing
alignment
updated 4.8 years ago by
Biostar
20 • written 4.8 years ago by
dbready2
• 0
0
votes
5
replies
1.4k
views
Multivariable multi sequence alignment
alignment
sequence
updated 4.8 years ago by
Joe
22k • written 4.8 years ago by
benoitdav
• 0
0
votes
1
reply
2.1k
views
cutadapt doesn't trim all primers
R
sequencing
updated 4.8 years ago by
lieven.sterck
16k • written 4.8 years ago by
fladveronika
• 0
0
votes
0
replies
679
views
Finding Entrez geneIDs from a GEO expression set object in R
GEO
R
updated 4.8 years ago by
GenoMax
154k • written 4.8 years ago by
petrandent
▴ 50
1
vote
7
replies
3.7k
views
Extracting group-specific combinations from distance matrix
R
4.8 years ago by
mario_de_manner
▴ 20
0
votes
0
replies
763
views
Naming deletion resulting in premature stop gained mutation
hgvs
variant nomenclature
4.8 years ago by
arunkumarramrsh
▴ 40
5
votes
1
reply
2.6k
views
10 follow
How to delete my biostars account?
meta
biostars
updated 18 months ago by
Istvan Albert
103k • written 6.8 years ago by
brunaz
▴ 20
1
vote
1
reply
1.2k
views
How to install TMAP
alignment
next-gen
sequencing
Assembly
4.8 years ago by
Nobody
▴ 30
1
vote
2
replies
1.0k
views
Metagenomics: classification analysis
sequencing
4.8 years ago by
valentinav
• 0
0
votes
2
replies
1.1k
views
Chip-seq peak calling best way usage of parameters
ChIP-Seq
4.8 years ago by
luckysardar171
▴ 20
2
votes
1
reply
2.0k
views
Meaning of shared alternate location indicator between residues in PDB format
pdb
atomic-coordinates
alternate-location
4.8 years ago by
Pshenichnaya
▴ 10
0
votes
3
replies
870
views
RNA-SEQ: Low % of Alignment
RNA-Seq
rna-seq
4.8 years ago by
ankit.n
• 0
2
votes
1
reply
1.3k
views
WGCNA with low number of samples
RNA-Seq
WGCNA
4.8 years ago by
dahun73
▴ 10
0
votes
0
replies
756
views
Visualization of common pathways
visualization
updated 2.7 years ago by
Ram
45k • written 4.8 years ago by
mrashad
▴ 80
0
votes
0
replies
475
views
About peptide design
software error
4.8 years ago by
fatema19.bge
• 0
1
vote
2
replies
1.8k
views
how can I interpret DEG value and p value in RNAseq
RNA-Seq
edgeR
updated 4.8 years ago by
swbarnes2
15k • written 4.8 years ago by
progistar
▴ 40
2
votes
5
replies
5.4k
views
MEGA X ERROR MUSCLE Log file did not end properly
MEGAX
MUSCLE
alignment
software error
4.8 years ago by
geshapiro01
• 0
3
votes
3
replies
2.0k
views
Annotating gene names: Why having different number of ensembl IDs using biomaRt
rna-seq
R
gene
updated 4.8 years ago by
jared.andrews07
★ 19k • written 4.8 years ago by
Ridha
▴ 130
2
votes
0
replies
1.9k
views
Job:
Evolutionary Genomics - Bioinformatics Researcher - U. Wisconsin
Assembly
genome
madison
Drosophila
updated 2.7 years ago by
Ram
45k • written 4.8 years ago by
jpool
▴ 20
1
vote
4
replies
3.2k
views
Cell annotation in Single Cell RNA seq
R
rna-seq
updated 4.8 years ago by
jared.andrews07
★ 19k • written 4.8 years ago by
rogerbear
▴ 30
0
votes
2
replies
1.2k
views
how to plot a heatmap with out dendogram using function TOMplot() in WGCNA
WGCNA
heatmap
r
4.8 years ago by
adR
▴ 130
0
votes
2
replies
2.8k
views
Error in creating the standard Kraken2 database
kraken2
plasmid
format violated
updated 4.8 years ago by
GenoMax
154k • written 4.8 years ago by
nathaliaoliveira
• 0
0
votes
2
replies
2.7k
views
Is the most recent Normd version (1.3) missing the executable to remove badly aligned sequences?
sequence
alignment
updated 3.3 years ago by
Ram
45k • written 10.0 years ago by
ronaldnieuwenhuis
▴ 30
0
votes
1
reply
1.2k
views
Count the length of a sequence and sort it into a multifasta file
Biopython
Sequence
Count
Length
updated 4.8 years ago by
Mensur Dlakic
★ 30k • written 4.8 years ago by
diego1530
▴ 80
1
vote
2
replies
1.1k
views
Mean sample depth?
depth
SNP
4.8 years ago by
giulia.trauzzi
▴ 30
0
votes
0
replies
1.4k
views
Job:
Ph.D./postdoc in structural bioinformatics and Molecular Dynamics
molecular-dynamics
structural-bioinformatics
updated 2.5 years ago by
Ram
45k • written 4.8 years ago by
Sergio Martínez Cuesta
▴ 230
0
votes
0
replies
639
views
mm_gene_length.txt for logCPM to FPKM
RNA-Seq
4.8 years ago by
tianmin1111
• 0
0
votes
0
replies
786
views
Package for transcript assembly of reference-aligned ion torrent reads
rna-seq
assembly
ion torrent
454
4.8 years ago by
cjwwfd
• 0
10
votes
4
replies
14k
views
Converting CRAM to BAM without reference fasta
samtools
BAM
CRAM
4.8 years ago by
Ld_60
▴ 80
0
votes
1
reply
736
views
Duplicate row names for gene names in DRInsight
RNA-Seq
updated 4.8 years ago by
matt_hias
• 0 • written 4.8 years ago by
j.hoolachan
▴ 10
0
votes
1
reply
1.2k
views
Problem using load_raw() function in crossmeta R package
crossmeta
R
meta-analysis
4.8 years ago by
michael.s
▴ 10
3
votes
5
replies
1.7k
views
Slicing Genbank File by range
sequence
extract
gbk
python
4.8 years ago by
kamel
▴ 70
2
votes
2
replies
3.6k
views
featureCounts paired end mode
featureCounts
subread
bam
paired
RNA-Seq
updated 4.8 years ago by
Carlo Yague
9.0k • written 4.8 years ago by
henry-keen
▴ 50
1
vote
1
reply
2.2k
views
Using GRch38 (human genome) primary assembly for mapping long reads
assembly
alignment
updated 4.8 years ago by
colindaven
8.1k • written 4.8 years ago by
prasundutta87
▴ 730
0
votes
1
reply
2.3k
views
What number I should specify for SMARTer Stranded Total RNA-Seq Kit v2 for --forward-prob in RSEM?
RNA-Seq
rna-seq
updated 4.8 years ago by
tjbencomo
▴ 70 • written 5.9 years ago by
John
▴ 280
0
votes
6
replies
4.0k
views
DESeqDataSetFromMatrix error: invalid 'row.names'
R
rna-seq
4.8 years ago by
jschiant
• 0
0
votes
1
reply
993
views
Does Illumina's bcl2fastq command line tool have a way to pipe to stdout immediately
bcl2fastq
illumina
next-gen
4.8 years ago by
b10hazard
• 0
0
votes
0
replies
1.2k
views
Job:
Two Senior Bioinformatics Scientist positions at AstraZeneca (Cambridge, UK)
cheminfomatics
AstraZeneca
updated 2.7 years ago by
Ram
45k • written 4.8 years ago by
Sergio Martínez Cuesta
▴ 230
1
vote
2
replies
1.2k
views
Convergence issues in Admixture software
admixture
4.8 years ago by
rakinitopo
▴ 10
122,217 results • Page
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Recent Votes
Comment: circos plot for genomic features
Answer: How to perform GO enrichment in non-model organisms?
Comment: circos plot for genomic features
Answer: How excactly is the Q30 is calculated?
A: PCA in a RNA seq analysis
what cause poly-G from NextSeq
what cause poly-G from NextSeq
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Comment: Issue while running Kenddata.
by
GenoMax
154k
Look inside the `*.log` files to see if you can get additional clues (and post them here, if you can't figure out things). Check for lines …
Comment: Question about QC and scrublet
by
Arup Ghosh
3.5k
You can run Scrublet before filtering cells with high gene counts and compare the doublet score vs `n_counts_genes`.
Answer: How to perform GO enrichment in non-model organisms?
by
lieven.sterck
16k
In first instance you will as you say need to assign GOterms to your genes. eggNOG-mapper is certainly a valid approach to do this indeed. …
Comment: circos plot for genomic features
by
Matteo Ungaro
▴ 140
@colindaven thanks a lot! `clinker` also seems to be a nice/effective tool to do so. It happens we stuble across a work where they used `Ci…
Comment: circos plot for genomic features
by
colindaven
8.1k
Why not use something like Jbrowse2 instead ? https://jbrowse.org/jb2/gallery/ You can load both haplotypes, use minimap2 to create a paf …
Comment: How excactly is the Q30 is calculated?
by
colindaven
8.1k
This is really a question for your instrument provider. Only MGI application specialists and their bioinformaticians can really answer this…
Answer: How excactly is the Q30 is calculated?
by
GenoMax
154k
[**Phred quality scores**][1] have been in use since the 1990s and early days of human genome project. They were co-opted in the fastq form…
Comment: best practice for diploid variant calling
by
Matteo Ungaro
▴ 140
@kevin thanks I was experimenting with the following since I already pursued most of the approaches you mentioned and, in practice, they ar…
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 !
Answer: 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…
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