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122,200 results • Page
612 of 2444
Sort: Rank
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Votes
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0
votes
1
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1.4k
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EdgeR - Input for Analysis Functions (estimateDisp, exactTest, glmQLFit)
edgeR
R
4.3 years ago by
Noah E.
▴ 20
1
vote
1
reply
1.3k
views
How to change CpG methylation cutoffs in edgeR
R
updated 4.3 years ago by
iraia.munoa
▴ 130 • written 5.6 years ago by
embueno
• 0
1
vote
5
replies
2.8k
views
MUSCLE alignment - aligning whole genome with gene sequences
alignment
mega
updated 4.3 years ago by
GenoMax
154k • written 4.3 years ago by
manaswwm
▴ 570
5
votes
4
replies
3.4k
views
Error when using UpSetR package
UpSetR
R
4.3 years ago by
peter.berry5
▴ 60
18
votes
15
replies
21k
views
9 follow
Tools Parsing Ncbi Blast -M 7 Xml Output Format?
blast
xml
parsing
updated 4.3 years ago by
Yoann Pageaud
• 0 • written 14.6 years ago by
Lhl
▴ 760
0
votes
8
replies
2.1k
views
print only columns with data from every line
unix
awk
4.3 years ago by
HL
▴ 10
2
votes
12
replies
3.9k
views
Bowtie2 aligner
Bowtie2
alignment
updated 4.3 years ago by
GenoMax
154k • written 4.3 years ago by
priya.bmg
▴ 70
1
vote
2
replies
1.1k
views
Determine relative copy numbers of plasmids
mapping
bowtie2
samtools
coverage
4.3 years ago by
rororo
▴ 10
0
votes
1
reply
1.1k
views
SNP density plot of aedes genome using bed file
density
Variant
ideograms
4.3 years ago by
anithanagaraj93
▴ 10
1
vote
0
replies
816
views
What is the importance of removing reads mapped to repetitive elements for downstream enrichment in RNAseq/CLIPseq?
Repetitive_elements
alignment
CLIPseq
RNAseq
updated 4.3 years ago by
GenoMax
154k • written 4.3 years ago by
Patrick
▴ 10
1
vote
1
reply
1.3k
views
How to get uniform data yields per barcode in nanopore sequencing
ONT
nanopore
updated 4.3 years ago by
samuel.a.odonnell
▴ 640 • written 4.3 years ago by
Irsan
★ 7.8k
0
votes
0
replies
1.1k
views
Job:
PhD student, PostDoc and Software Developer Positions at the interface of Mathematics and Life Science
postdoc
phd
Computational-Biology
Mathematics
updated 2.7 years ago by
Ram
45k • written 4.3 years ago by
emad-24
• 0
0
votes
0
replies
792
views
somatic variant calling with Mutect2
calling
somatic
Mutect2
variant
4.3 years ago by
Elisa
• 0
0
votes
0
replies
732
views
Forum:
Poll about a structured description of a tool, a pipeline
survey
pipeline
updated 2.4 years ago by
Ram
45k • written 4.3 years ago by
Anastasiya M
• 0
1
vote
11
replies
3.4k
views
How to merge folders that have similar (not the same) names, in a folder keeping as its name the common part of the name of the two folders
folders
merge
name-based
updated 4.3 years ago by
cpad0112
21k • written 4.3 years ago by
Mania
• 0
4
votes
5
replies
1.5k
views
6 follow
Gene prediction methods
Gene
prediction
updated 4.3 years ago by
GenoMax
154k • written 4.4 years ago by
Pratheep
▴ 150
1
vote
4
replies
2.5k
views
cellranger count aggregated to transcripts
cellranger
gtf
10x
updated 4.3 years ago by
benformatics
4.2k • written 4.3 years ago by
jomo018
▴ 730
1
vote
4
replies
2.2k
views
Paired-end to Single-end
bam
updated 4.3 years ago by
Kevin Blighe
★ 90k • written 4.3 years ago by
kstangline
▴ 110
1
vote
4
replies
2.6k
views
extracting fasta sequence from fasta file with multiple genomes
bedtools
fasta
grep
updated 4.3 years ago by
cpad0112
21k • written 4.3 years ago by
ss3943
• 0
0
votes
0
replies
781
views
Repeat masking custom library not reading
masking
repeat
ngs
repeatmasker
4.3 years ago by
Shri hari
▴ 40
8
votes
10
replies
3.3k
views
FASTA of translated amino acid sequences in their six reading frames, which one is the optimal?
aminoacid
protein
peptide
Reading
optimal
frames
4.3 years ago by
Luis999
▴ 20
0
votes
4
replies
2.3k
views
kissplice2reftranscriptome interpreting output
RNA-Seq
kissplice2reftranscriptome
kissplice
updated 4.3 years ago by
944908620
• 0 • written 7.8 years ago by
rares_lucaciu
• 0
0
votes
0
replies
1.0k
views
PSMC parameter choosing (-t, -p)
psmc
updated 2.7 years ago by
Ram
45k • written 4.3 years ago by
clinnaeus
▴ 30
9
votes
5
replies
30k
views
7 follow
DESeq2 analysis for multiple conditions
RNA-Seq
DESeq2
updated 2.9 years ago by
Ram
45k • written 10.5 years ago by
eager_learner
▴ 60
0
votes
1
reply
1.6k
views
Help with installing Bayescan (Big Sur)
Installation
commandline
Bayescan
updated 4.3 years ago by
ATpoint
90k • written 4.3 years ago by
8bde229f
• 0
2
votes
2
replies
1.4k
views
Functional annotation by blast
trembl
Blast
nr
Functional_annotation
Blast2GO
4.3 years ago by
GenesisBio
• 0
0
votes
0
replies
1.7k
views
Job:
Senior Postdoctoral Research Fellow at Big Data Institute, University of Oxford
big
postdoc
genomics
data
4.3 years ago by
Shicheng Guo
★ 9.6k
0
votes
1
reply
1.6k
views
What does betaPrior do in DESEQ?
DESeq
RNAseq
updated 4.3 years ago by
i.sudbery
22k • written 4.3 years ago by
kirby199
• 0
0
votes
0
replies
974
views
Herald:
The Biostar Herald for Monday, July 26, 2021
herald
4.3 years ago by
Biostar
3.7k
0
votes
1
reply
1.0k
views
Handling cultivars in transcriptome de novo assembly
transcriptomic
trinity
DGE
updated 4.3 years ago by
h.mon
35k • written 4.3 years ago by
DaneLukin
• 0
0
votes
1
reply
907
views
Quantify the effects of a gene list between datasets
scRNA-Seq
Comparison
RNA-Seq
4.3 years ago by
bioinf.questions
• 0
4
votes
4
replies
2.2k
views
RNA-seq for samples with RIN<3
RIN
Low
updated 10 months ago by
Emilie
▴ 10 • written 4.3 years ago by
mariam28071993
• 0
1
vote
1
reply
835
views
How can I extract duplicated rows for the same value and write them down in one row
bash
updated 4.3 years ago by
Ram
45k • written 4.3 years ago by
amal.elzemrany
▴ 30
3
votes
3
replies
2.2k
views
How do you split metagenomic bins/MAGs into eukaryotic and prokaryotic?
protist
metagenomics
prokaryotic
eukaryotic
gtdbtk
updated 4.3 years ago by
Mensur Dlakic
★ 30k • written 4.3 years ago by
O.rka
▴ 750
2
votes
2
replies
1.2k
views
Helper packages for differential gene expression analysis in R
dge
deseq2
RNA-seq
r
updated 4.3 years ago by
GenoMax
154k • written 4.3 years ago by
Dunois
★ 2.9k
0
votes
0
replies
666
views
How can I conduct GO/Pathway analysis in EdgeR when there is >1 value for each gene?
edgeR
R
4.3 years ago by
Noah E.
▴ 20
1
vote
0
replies
703
views
GO Term analysis
GO
updated 4.3 years ago by
Ram
45k • written 4.3 years ago by
snehu.sambare
▴ 10
1
vote
2
replies
1.9k
views
Merge regions in bedgraph file
bedgraph
4.3 years ago by
eoneill627
▴ 20
0
votes
0
replies
961
views
Paired Analysis in EdgeR
EdgeR
PairedAnalysis
4.3 years ago by
bryan.yankee27
• 0
1
vote
2
replies
1.1k
views
Low similarity gene alignment
analysis
align
gene
updated 4.3 years ago by
Dunois
★ 2.9k • written 4.3 years ago by
Hsiangnan Cheng
• 0
0
votes
1
reply
1.1k
views
metascape
list
gene
input
metascape
updated 4.3 years ago by
Ram
45k • written 4.3 years ago by
fionajcunningham
• 0
5
votes
5
replies
4.6k
views
Visualiation of samtools depth output in a plot
plot
depth
samtools
updated 4.1 years ago by
Carlo Yague
9.0k • written 4.3 years ago by
dominik.lagler
▴ 30
1
vote
3
replies
1.3k
views
ALT-aware autodetection of hg38.p13 in DRAGEN
alt
patch
alt-aware
dragen
hg38
updated 4.3 years ago by
GenoMax
154k • written 4.3 years ago by
Tal
• 0
0
votes
0
replies
1.2k
views
Error with CONVERTF mergeit program
plink
convertf
eigenstrat
4.3 years ago by
harmadikemil
• 0
2
votes
2
replies
1.3k
views
Filter vcf file based on the GTs of a single sample
bcftools
vcf
samtools
bcf
updated 4.3 years ago by
sbstevenlee
▴ 480 • written 4.3 years ago by
miguellarrazlopezdenovales
▴ 20
4
votes
6
replies
2.9k
views
6 follow
What is the best annotation tool?
VCF
annotation
updated 4.3 years ago by
colindaven
8.1k • written 4.3 years ago by
Sonia
• 0
0
votes
0
replies
1.0k
views
Job:
Postdoctoral Fellowship in Bioinformatics and Liver Cancer Genomics
Cancer
NGS
Single-cell
genomics
updated 2.7 years ago by
Ram
45k • written 4.3 years ago by
waihungh
▴ 20
0
votes
0
replies
1.7k
views
Job:
PhD Scholarship in Bioinformatics and Liver Cancer Genomics
Cancer
NGS
Single-cell
genomics
updated 2.7 years ago by
Ram
45k • written 4.3 years ago by
waihungh
▴ 20
0
votes
0
replies
931
views
Job:
research assistant in bioinformatics at Essen University Hospital
metadata
Germany
Essen
updated 2.7 years ago by
Ram
45k • written 4.3 years ago by
christina.klaere
• 0
1
vote
6
replies
7.7k
views
How to write a .pdb file using Python
python
PDB
output
updated 4.3 years ago by
Nitin Narwade
★ 1.7k • written 4.3 years ago by
Jingtong
• 0
122,200 results • Page
612 of 2444
Recent Votes
strong appearing variant not found by haplotypecaller in -ERC mode and deepvariant but with haplotypecaller in normal mode
Answer: How can I easily remove overlapping transcripts, keeping only longest transcript
Answer: Log2 transformation is well used, but is there a good paper that can be used as
Answer: Flatten a GTF
Answer: RNA-seq - Creating SAF from NCBI gff for Subread featureCounts - keep 'gene' or
Can EdgeR of DeSeq be used for Single-cell RNA-seq?
Answer: Getting the overlap between two GTF files
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Recent Replies
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Wu-Sheng Zhang
• 0
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…
Comment: Subsetting before QC in Spatial Transcriptomics
by
Kent
▴ 30
Hi Kevin, Thanks for the detailed explanation. Due to the characteristics of the datasets, we initially used very lenient quality control…
Comment: Midpoint rooting IQTREE newick file moves node support around
by
Luca Arbore
▴ 10
Thank you very much Kevin, it worked!
Comment: ID unifiying across different datasets
by
GenoMax
154k
In this case the entry notes that this is likely the product of a pseudogene: https://www.uniprot.org/uniprotkb/Q5VTE0/entry and existence …
Comment: Comparison of different RNAseq data sets
by
DrSmad
▴ 10
Each lab contributes both control and LPS. Example, for cell line A_lab1 did and analysis on control and LPS-6h. Cell line B_lab2 did contr…
Comment: ID unifiying across different datasets
by
zizigolu
★ 4.4k
sorry, why some gene names are often lacking though the Uniprot ID is still valid (using biomart)?
Comment: snpEff: Unsupported structural variant types
by
shpak.max
▴ 70
Unfortunately, while it ran without a problem initially, when I checked the run screen today, I saw the following error message (and unlike…
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