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122,211 results • Page
699 of 2445
Sort: Rank
Rank
Views
Votes
Replies
12
votes
8
replies
7.5k
views
Is there a way to visualize log fold changes for Reactome pathways in R?
pathview
RNA-Seq
reactome
bioconductor
updated 4.7 years ago by
bigmawen
▴ 440 • written 6.6 years ago by
Gabriel
▴ 180
0
votes
1
reply
1.2k
views
Is there any way to access the --cores argument in a snakemake workflow?
snakemake
updated 3.9 years ago by
Eugene A
▴ 190 • written 4.7 years ago by
curious
▴ 900
2
votes
2
replies
1.0k
views
Sequencing Information from BAM file
RNA-Seq
BAM
alignment
Library
4.7 years ago by
MarVi
▴ 30
8
votes
10
replies
2.4k
views
Performing Differential expression analysis using DESeq with 3 conditions
RNA-Seq
Deseq2
R
next-gen
bioconductor
4.7 years ago by
bionewbie
• 0
0
votes
2
replies
1.0k
views
Identifiying SNP frequencies for very specific subpopulations on dbSNP
SNP
4.7 years ago by
Michael
▴ 290
3
votes
3
replies
2.5k
views
Counts alongside Fold changes - FindMarkers Seurat
RNA-Seq
seurat
4.7 years ago by
ishwariyavenkatesh
• 0
0
votes
0
replies
656
views
Statistical correlation for in-group vs outgroup trait frequencies
statistics
p-value
spearman correlation
4.7 years ago by
leonid.rusin
• 0
0
votes
0
replies
663
views
Normalization for WGCNA on two organisms (virus-host)
RNA-Seq
DESeq2
WGCNA
Normalization
updated 4.7 years ago by
Biostar
20 • written 4.7 years ago by
robert.buecking
• 0
2
votes
1
reply
1.5k
views
plink --indep LD calculation and filtering to VCF file in one command
plink
4.7 years ago by
rjzotti
• 0
1
vote
6
replies
3.5k
views
Setting genotypes to missing for certain positions in vcf file
vcf
vcftools
updated 4.7 years ago by
Pierre Lindenbaum
166k • written 4.7 years ago by
jtull
• 0
6
votes
3
replies
12k
views
The fastest way to download a list of SRR accessions from Sequence Read Archive with sratoolkit
sequence
genome
updated 4.7 years ago by
kostaspildish
▴ 20 • written 5.9 years ago by
Denis
▴ 320
3
votes
2
replies
4.6k
views
Can't create tabix index of the bed file
samtools
tabix
bed
ATAC-seq
updated 4.7 years ago by
desouzareis.r
▴ 290 • written 4.7 years ago by
i.am.filippov
▴ 10
0
votes
5
replies
1.4k
views
Shrunk data from Novogene
RNA-Seq
4.7 years ago by
Futuremaking
• 0
1
vote
2
replies
1.7k
views
scRNA cross-species integration using Seurat v3
integration
scRNA-Seq
FindIntegrationAnchors
4.7 years ago by
maddhesiya13
• 0
5
votes
8
replies
2.6k
views
A layman trying to understand what a FASTA file is
RNA-Seq
gene
next-gen-sequencing
updated 2.7 years ago by
Ram
45k • written 4.7 years ago by
GoldenRetriever
▴ 40
0
votes
3
replies
1.9k
views
change missing genotype in bcf file from 0/0 to ./. to run plink
bcftools
plink
SNP
genotype
bcf
4.7 years ago by
rah
▴ 30
0
votes
1
reply
2.9k
views
BLAST error: Input db vol size does not match lmdb vol size
BLAST
Database
Error
Protein
NR
4.7 years ago by
Hansen_869
▴ 80
3
votes
3
replies
1.5k
views
installation of shovill on windows
software error
assembly
updated 4.7 years ago by
kapsakcj
▴ 90 • written 4.7 years ago by
Rima
▴ 20
0
votes
22
replies
4.5k
views
Specifying database path in BLAST standalone
blast
path
standalone
4.7 years ago by
Hansen_869
▴ 80
0
votes
0
replies
966
views
Plasmids in the Resfinder tool?
resfinder
sequencing
antibiotic
resistance
4.7 years ago by
Researcher
▴ 20
1
vote
1
reply
1.2k
views
CWL workflow - nested_crossproduct output
CWL
scatter
workflow
nested_crossproduct
updated 4.4 years ago by
Michael R. Crusoe
★ 1.9k • written 4.7 years ago by
cocchi.e89
▴ 300
2
votes
4
replies
1.3k
views
featurecounts -p Paried ends which count total to use as read1 &read 2 give different totals.
RNA-Seq
alignment
R
gene
sequencing
4.7 years ago by
ray.liv.wong
• 0
3
votes
3
replies
1.2k
views
How can the assumption of a broad/narrow peak be checked?
macs2
ChIP-Seq
4.7 years ago by
Aspire
▴ 390
1
vote
1
reply
1.1k
views
variant calling using masked reference genome
Bowtie2
Reference Genome
Variant Calling
4.7 years ago by
reza
▴ 300
7
votes
11
replies
4.6k
views
What is the appropriate approach for ChIPseq protein genome occupancy % calculation?
ChIP-Seq
updated 2.9 years ago by
Ram
45k • written 10.4 years ago by
AlexAbdulkaderKheirallah
▴ 120
4
votes
18
replies
5.2k
views
Want to reverse the fasta sequence
fasta
4.7 years ago by
harry
▴ 40
2
votes
4
replies
3.4k
views
Read VEP output from command line in R
vep
ensembl
R
Bash
updated 16 months ago by
mimarcelape
• 0 • written 4.7 years ago by
yussab
▴ 100
1
vote
2
replies
977
views
In-silico downsizing to estimate the DNA input
sequencing
snp
next-gen
updated 4.7 years ago by
5heikki
11k • written 4.7 years ago by
APJ
▴ 40
0
votes
6
replies
1.0k
views
How to get related proteins and gene data of an organism (for eg. Lactobacillus )
gene
genome
updated 4.7 years ago by
Joe
22k • written 4.7 years ago by
biostars_23e2e
• 0
3
votes
6
replies
5.7k
views
Is the ENSEMBL FTP down?
ensembl
ftp
updated 4.2 years ago by
rohitsatyam102
▴ 940 • written 4.7 years ago by
liorglic
★ 1.5k
0
votes
1
reply
1.0k
views
Kraken abundances do not add up
kraken2
4.7 years ago by
jsgounot
▴ 170
1
vote
1
reply
3.6k
views
Suggest vcf filtered parameter for gatk VariantFiltration
gatk4
snps
updated 4.7 years ago by
kanika.151
▴ 160 • written 6.5 years ago by
Mbillah
▴ 140
0
votes
0
replies
817
views
Run TSS predator without TEX wig libraries
RNA-Seq
sequencing
next-gen
software error
4.7 years ago by
qstefano
▴ 20
0
votes
1
reply
1.3k
views
Repeated measures in GWAS and polygenic risk scores analyses
SNP
updated 2.1 years ago by
zx8754
12k • written 5.7 years ago by
kl
▴ 20
0
votes
2
replies
2.0k
views
conversion of a genlight object into a genpop object
snp
R
updated 2.4 years ago by
Mike
• 0 • written 5.3 years ago by
satish.vety
• 0
0
votes
1
reply
2.7k
views
KEGG Reconstruct Pathway: More Efficient Usage
Kegg
Pathway
genome
updated 4.7 years ago by
Biostar
20 • written 8.3 years ago by
taylrtam
• 0
1
vote
2
replies
1.4k
views
Data normalization (raw counts) and DEG analysis. Do I have a problem with my pipeline?
R
RNA-Seq
4.7 years ago by
Peter
▴ 20
0
votes
0
replies
1.1k
views
Is it possible to call variants using cram files?
next-gen
sequencing
SNP
4.7 years ago by
vinayjrao
▴ 260
32
votes
34
replies
19k
views
10 follow
How To Randomly Sample A Subset Of Lines From A Bed File
bed
chip-seq
updated 4.1 years ago by
Ram
45k • written 12.1 years ago by
bede.portz
▴ 540
1
vote
3
replies
3.9k
views
Meme/Ame - bad file error
meme
ame
motif
4.7 years ago by
LacquerHed
▴ 30
6
votes
8
replies
2.2k
views
What does mean HHHHHH in structures?
structure
protein
pdb
updated 4.7 years ago by
Mensur Dlakic
★ 30k • written 4.7 years ago by
Xylanaser
▴ 80
0
votes
1
reply
2.5k
views
ERROR UTR only implemented with shadow and partial or complete. Augustus
busco
Augustus
updated 4.7 years ago by
boymin2020
▴ 80 • written 5.6 years ago by
18140010
• 0
5
votes
2
replies
1.1k
views
NCBI genome stats
genome
stats
ncbi
updated 4.7 years ago by
GenoMax
154k • written 4.7 years ago by
Chirag Parsania
★ 2.0k
0
votes
0
replies
1.1k
views
gromacs: RNA-Protein interaction
gromacs
RNA
Protein
updated 4.7 years ago by
Biostar
20 • written 4.9 years ago by
aminijavad4
▴ 10
4
votes
10
replies
2.9k
views
Importing quant.sf file to tximport
software-error
tximport
genome
updated 2.5 years ago by
Ram
45k • written 4.7 years ago by
yvarg009
• 0
2
votes
2
replies
2.1k
views
Deleting text from row.names in a dataframe
RNA-Seq
4.7 years ago by
salehm
▴ 10
0
votes
1
reply
1.2k
views
Docker image exceRpt pipeline help
docker
small RNA seq
RNAseq
exceRpt
updated 4.7 years ago by
vimalkvn
▴ 320 • written 4.7 years ago by
enh
• 0
3
votes
3
replies
2.0k
views
How to concatenate multiple fastq files (located in different directories) for each sample
RNA-Seq
updated 4.7 years ago by
rpolicastro
13k • written 4.7 years ago by
salehm
▴ 10
0
votes
6
replies
2.0k
views
Running PHG with singularity: Error at CreatePHG_step2_addHapsFromGVCF
PHG
singularity
4.7 years ago by
bp
• 0
2
votes
2
replies
1.5k
views
chr20_KI270871v1_alt in HG38 Broad Variant and Blacklist regions
ChIP-Seq
4.7 years ago by
ahadli.farid
▴ 50
122,211 results • Page
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Recent Replies
Comment: best practice for diploid variant calling
by
Matteo Ungaro
▴ 130
@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
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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
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▴ 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
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(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
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▴ 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
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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.
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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
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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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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…
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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
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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
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thomas.heigl.ibk
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here the igv view. showing the histogram for all samples plus the reads for one: ![enter image description here][1] and expanded view of …
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3.5k
Check the read lengths to make sure the files are correct.
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by
alexandrakortsi
• 0
By sequence. Thank you for your response!
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