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122,213 results • Page
704 of 2445
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
848
views
Variant Calling when Genetic Distance between Reference and Samples is Greater than it is for Humans: Does GATK still perform well?
GATK
variant calling
MASH
4.7 years ago by
robertwhbaldwin
• 0
1
vote
1
reply
687
views
Gene names from gene ID
gene
alignment
4.7 years ago by
shivam.jgandhi
• 0
0
votes
1
reply
984
views
Plot fastPHASE output
fastphase
plot
R
haplogroups
SNP
updated 4.7 years ago by
nbkingsley
• 0 • written 4.7 years ago by
simone.castellana
▴ 10
0
votes
0
replies
762
views
How to analyze ribosome profiling data in the form of a 2x2x2 experiment
RNA-Seq
Ribosome Profiling
DESeq2
4.7 years ago by
kyusikkim
▴ 20
0
votes
2
replies
970
views
How can I ask questions that contain species names?
meta
updated 2.5 years ago by
Ram
45k • written 4.7 years ago by
garden_giessen
▴ 130
9
votes
11
replies
4.3k
views
I cannot open jalview on linux
ubuntu
java
jalview
updated 4.7 years ago by
ben_s
▴ 50 • written 4.7 years ago by
hamid.gaikani
▴ 80
0
votes
0
replies
1.0k
views
Job:
Senior Bioinformatics Scientist at Boston Children's Hospital
scRNA-seq
next-gen
RNA-Seq
updated 2.7 years ago by
Ram
45k • written 4.7 years ago by
shira.rockowitz
▴ 10
2
votes
4
replies
1.5k
views
Compare different library
RNA-Seq
DESeq2
updated 4.7 years ago by
Biostar
20 • written 6.1 years ago by
inminin
• 0
0
votes
0
replies
1.4k
views
filtering issue when using bamCoverage
alignment
sequencing
bam
bamCoverage
deepTools
4.7 years ago by
GA
• 0
2
votes
3
replies
948
views
Find defence related and disease resistant genes in Rice genome
genome
gene
sequence
4.7 years ago by
vedikaa96
• 0
1
vote
1
reply
1.3k
views
Job:
Opportunity: Bioinformatics Engineer - Bioinformatics Core @ Memorial Sloan Kettering Cancer Center, New York, NY (US)
cancer-biology
Python
R
updated 2.7 years ago by
Ram
45k • written 4.7 years ago by
bic-recruit
▴ 10
0
votes
3
replies
878
views
How can I download the essential list of medicines of Germany without paying fees?
atc
atccodes
essentialmedicines
activeingredients
updated 4.7 years ago by
GenoMax
154k • written 4.7 years ago by
victoria.r.ibarra
• 0
2
votes
1
reply
2.0k
views
Cytoscape - how do I change the node size relative to number of edges?
cytoscape
software-error
updated 2.7 years ago by
Ram
45k • written 4.7 years ago by
gemmalouisebaldock
▴ 20
0
votes
0
replies
904
views
Job:
Postdoctoral Research Fellow position in neurodevelopmental genetics research
R
genome
next-gen
updated 2.3 years ago by
Ram
45k • written 4.7 years ago by
ryan.yuen
• 0
3
votes
4
replies
13k
views
What absolute copy number would you call an Amplification?
SNP
genome
snparray
copy-number
updated 3.7 years ago by
Ram
45k • written 10.9 years ago by
senowinski
▴ 30
1
vote
2
replies
966
views
I carried out a BLASTp search for protein A1 from organism A. It produced a match for protein B1 from organism B. When I then conducted a BLASTp sear…
BLAST
sequence
protein
BLASTp
gene
4.7 years ago by
anna.dowd
• 0
0
votes
4
replies
1.3k
views
Package lncDIFF input files format
RNA-Seq
updated 2.5 years ago by
Ram
45k • written 4.7 years ago by
valopes
▴ 30
0
votes
0
replies
713
views
Silent error in CNVkit genemetrics
cnvkit
software error
4.7 years ago by
apmills
• 0
0
votes
0
replies
1.4k
views
GWAS q-q plot showing lots of "1's" and a flat line with logistic regression
gwas
qqplot
plink
4.7 years ago by
Vanish007
▴ 50
3
votes
7
replies
2.8k
views
DiffBind analysis - minCount parameter in dba.count()
ChIP-Seq
DiffBind
3.7 years ago by
vk
▴ 40
6
votes
2
replies
1.8k
views
Concatenating single gene alignments
Panaroo
Multiple sequnce alignment
MSA
R
updated 4.7 years ago by
Ram
45k • written 4.7 years ago by
matejasoretic
▴ 10
0
votes
0
replies
1.8k
views
Cannot recalculate Kimura distance values - Repeatmasker
genome
repeats
repeatmasker
4.7 years ago by
panosprov
▴ 10
6
votes
23
replies
4.2k
views
Removing Illumina PCR primer sequences from TSA for GenBank upload
GenBank
assembly
primer
4.7 years ago by
Michael
56k
0
votes
3
replies
3.6k
views
Problems specifying data.type and sample.type in TCGAbiolinks GDCquery
tcga
tcgabiolinks
r
updated 21 months ago by
jain72744
▴ 10 • written 4.7 years ago by
loughrae
▴ 90
0
votes
0
replies
1.3k
views
Mutect2 failing to produce F1R2.tar.gz and stat files on TCGA bams (tumor-normal pairs)
next-gen
mutect2
updated 4.7 years ago by
GenoMax
154k • written 4.7 years ago by
tb_2020
• 0
0
votes
4
replies
2.1k
views
RNA-SEQ data, reads count zero
RNA-Seq
updated 4.7 years ago by
EagleEye
7.6k • written 4.7 years ago by
wschen97
• 0
5
votes
2
replies
2.5k
views
RNA-Seq data, batch effect source
RNA-Seq
updated 4.7 years ago by
Biostar
20 • written 8.3 years ago by
lu.ne
▴ 70
6
votes
4
replies
1.9k
views
Cytoscape - long list of proteins, very messy result
software error
4.7 years ago by
gemmalouisebaldock
▴ 20
0
votes
0
replies
991
views
Q-Q plot for p-value from HWE exact test
Q-Q plot
Hardy-Weinberg
p-value
GWAS
QC
4.7 years ago by
panacotaforcota
• 0
0
votes
0
replies
677
views
Reference gffs for jitterbug
jitterbug
MEl
WES
4.7 years ago by
Paso
▴ 10
0
votes
0
replies
1.2k
views
FIMO --max-stored-scores option
fimo
meme
4.7 years ago by
lessismore
★ 1.4k
1
vote
5
replies
1.3k
views
Mugsy percentage of identity
Mugsy
Genome-alignment
updated 2.2 years ago by
Ram
45k • written 4.7 years ago by
A_heath
▴ 180
3
votes
6
replies
2.3k
views
microrna mRNA interactions search
microrna
mrna
updated 4.6 years ago by
i.sudbery
22k • written 4.7 years ago by
cagdas
▴ 10
0
votes
0
replies
1.1k
views
variant calling error with VarDict
R
software error
snp
4.7 years ago by
shubhamkumbhar420
▴ 40
3
votes
2
replies
2.7k
views
ATAC-seq FastQC showing 5' sequence content bias
ATAC-seq
fastqc
updated 4.7 years ago by
ATpoint
90k • written 4.7 years ago by
Papyrus
★ 3.1k
3
votes
3
replies
1.3k
views
Samtools sort by name - bam size issue
alignment
genome
samtools
updated 4.7 years ago by
Pierre Lindenbaum
166k • written 4.7 years ago by
quentin54520
▴ 120
0
votes
1
reply
1.2k
views
metaphlan2.py ERROR: Unable to create folder for database install
genome
metagenome
4.7 years ago by
kocharovskayaj
• 0
3
votes
6
replies
2.5k
views
should I merge several SRR fastq file download from sra?
RNA-Seq
updated 4.7 years ago by
lieven.sterck
16k • written 4.7 years ago by
hellocita
▴ 40
3
votes
4
replies
2.1k
views
Unused command line option: --make-just-fam
plink
GWAS
linux
updated 4.7 years ago by
davidenoma
▴ 50 • written 4.7 years ago by
suraj.adewale1
• 0
2
votes
2
replies
1.2k
views
Remove fasta sequence on the basis of header name
fasta
header
updated 4.7 years ago by
5heikki
11k • written 4.7 years ago by
harry
▴ 40
2
votes
8
replies
4.6k
views
R script for loading .CEL.gz files in afffy package
R
microarray data
.CEL files
affy package
4.7 years ago by
raavi21198
▴ 20
0
votes
1
reply
1.1k
views
GWAS LocusZoom Plot from .CSV
gwas
plotting
updated 3.4 years ago by
El Rishi
• 0 • written 4.7 years ago by
abyousaf
• 0
2
votes
9
replies
6.2k
views
Allele count from factor variable in R
genome
SNP
R
updated 2.8 years ago by
Ram
45k • written 10.5 years ago by
pifferdavide
▴ 110
0
votes
2
replies
3.0k
views
Is it worth to analyzing low quality ATAC-seq data
ATAC-seq
QC
TSS
4.7 years ago by
cwwong13
▴ 40
1
vote
0
replies
1.1k
views
Single-cell-ATAC normalization and merginig
next-gen
R
sequencing
4.7 years ago by
C4
▴ 30
1
vote
3
replies
1.9k
views
How to extract the longest CDS from Homo_sapiens.GRCh38.cds.all.fa?
python script
biopython
ensembl
4.7 years ago by
Enhancer
• 0
0
votes
0
replies
1.1k
views
TopMed VCF validation error
TopMed
VCF
Chunks
Validation
4.7 years ago by
Guilherme
▴ 40
0
votes
1
reply
750
views
How will the fusion sequence looks like in RNA level
rna-seq
next-gen
4.7 years ago by
sichen0415
• 0
1
vote
5
replies
1.4k
views
GO Terms - most common between - many gene lists (from 36 scRNAseq clusters)
RNA-Seq
next-gen
4.7 years ago by
kieran.short
• 0
0
votes
0
replies
869
views
Job:
HIRING: Sequencing Specialist - UC Santa Cruz Genomcis Institute
genome
RNA-Seq
assembly
illumina
sequence
updated 2.3 years ago by
Ram
45k • written 4.7 years ago by
genomicshr
▴ 30
122,213 results • Page
704 of 2445
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Recent Replies
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
▴ 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
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.
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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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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…
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by
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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
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…
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