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122,200 results • Page
661 of 2444
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Votes
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0
votes
1
reply
1.0k
views
What determine if a panel can be used for copy number analysis?
panel
copy
number
targeted
updated 4.5 years ago by
German.M.Demidov
★ 3.0k • written 4.5 years ago by
whb
▴ 60
2
votes
3
replies
2.0k
views
Need suggestions to combine the missense variants pathogenicity prediction scores generated by SIFT, CADD, REVEL, PolyPhen, MPC, etc. to prioritize/s…
Missense
PredictionTools
updated 4.4 years ago by
Ram
45k • written 4.5 years ago by
Apurba
▴ 10
1
vote
3
replies
2.5k
views
How to make a vcf file using GWAS Catalog all_association.tsv file
GWAS
VCF
genetic
association
CATALOG
updated 4.5 years ago by
Pierre Lindenbaum
166k • written 4.5 years ago by
Alexandros.Frydas
▴ 30
2
votes
2
replies
2.0k
views
gffread doesn't convert gff to gtf (blank file)
gffread
bash
updated 4.5 years ago by
Juke34
9.3k • written 4.5 years ago by
aka
▴ 10
0
votes
1
reply
1.2k
views
How to download dataset with paired 16S and shotgun from HMP?
16S
HMP
shotgun
4.5 years ago by
mail2steff
▴ 70
4
votes
10
replies
7.8k
views
how to use the samtools filtering expression ?
samtools
updated 2.7 years ago by
Ram
45k • written 4.5 years ago by
Hippolyte
• 0
0
votes
0
replies
648
views
Assemble 3'mRNAseq with standard RNAseq
stringtie
RNAseq
assembly
3mRNAseq
4.5 years ago by
Shred
★ 1.6k
1
vote
0
replies
1.0k
views
News:
Comprehensive benchmarking of software for mapping whole genome bisulfite data
Methylation
NGS
Epigenetics
Bisulfite
4.5 years ago by
David Langenberger
11k
0
votes
2
replies
1.6k
views
Find all genes in multiple regions
ucsc
ensembl
biomart
updated 4.5 years ago by
Jorge Amigo
14k • written 4.5 years ago by
brighteyes1017
• 0
2
votes
4
replies
1.9k
views
How to capture the position of SNPs from the gene's locations
Bedtools
Genome
SNPs
4.5 years ago by
Kumar
▴ 170
0
votes
0
replies
633
views
Many OTUs on chart
bracken
Megan
biom
kraken
updated 4.5 years ago by
ATpoint
90k • written 4.5 years ago by
Geyby Tatiana
• 0
1
vote
1
reply
868
views
Can I Illumina sequence with a polymerase that leaves -da overgangs?
sequencing
illumina
updated 4.5 years ago by
ATpoint
90k • written 4.5 years ago by
jomagrax
▴ 40
3
votes
6
replies
5.3k
views
Bamtools stats and samtools flagstat produce different results and confusing my sambamba output.
sambamba
bamtools
samtools
4.5 years ago by
DNAngel
▴ 260
1
vote
1
reply
1.4k
views
Pathway network
Reactome
Pathway
cytoscape
KEGG
igraph
updated 4.5 years ago by
Jean-Karim Heriche
27k • written 4.5 years ago by
Arindam Ghosh
▴ 550
0
votes
0
replies
898
views
porthomcl - executing only the certain step of procedures
threading
porthomcl
orthomcl
thread
4.5 years ago by
seok1213neo
▴ 40
0
votes
1
reply
1.1k
views
Error in using USEARCH - Bad line 5 in FASTQ file 'sample_R1.fastq': expected '@'
input
usearch
fastq
fastqfile
updated 4.5 years ago by
Mensur Dlakic
★ 30k • written 4.5 years ago by
Yu
• 0
3
votes
1
reply
1.9k
views
how to define open-pangenome?
python
fasta
genome
dna
clustering
updated 4.5 years ago by
Nelly
▴ 30 • written 4.7 years ago by
Kumar
▴ 120
1
vote
3
replies
1.3k
views
edgeR batch correction
edger
batch
4.5 years ago by
barix
▴ 20
0
votes
0
replies
707
views
Code for simulation of data sets
simulation
updated 4.5 years ago by
Ram
45k • written 4.5 years ago by
lorenzo
• 0
0
votes
1
reply
1.9k
views
Extracting Read and mates having variant positions Using BAM file vcf file in Python using pysam/ bamnostics
NGS_DATA
PYSAM
Python
BAM_FILE
updated 4.4 years ago by
Ram
45k • written 4.5 years ago by
Hassan
• 0
0
votes
0
replies
1.0k
views
Fatal error: exit code 1 () using make.shared
galaxy
metadata
metagenomics
mothur
error
4.5 years ago by
elfellah.aymane00
• 0
1
vote
2
replies
1.3k
views
how to identify if a contig.fa file comes from IDBA or Spades?
assembler
4.5 years ago by
leranwangcs
▴ 150
0
votes
9
replies
3.0k
views
How get density plot TSS region for genes of interest
Chipseq
updated 15 months ago by
QX
▴ 80 • written 4.5 years ago by
BISEP
▴ 10
2
votes
5
replies
2.1k
views
Best way to handle samples with both single end and paired end?
RNA-Seq
updated 4.5 years ago by
ATpoint
90k • written 4.5 years ago by
ichbinlynn93
▴ 30
1
vote
9
replies
3.5k
views
RNAseq: Modify .fasta and .gtf files to add recombinant protein sequence
reference
protein
modify
recombinant
4.5 years ago by
Pavlos
• 0
0
votes
0
replies
979
views
How can I summarize Log2 Fold Change values for many genes within a treatment group?
fold-change
updated 2.2 years ago by
Ram
45k • written 4.5 years ago by
sagrant
▴ 10
0
votes
1
reply
1.6k
views
Extract reads mapped within chosen intronic region from BAM file (no junctions)
bedtools
RNA-seq
samtools
updated 4.5 years ago by
Pierre Lindenbaum
166k • written 4.5 years ago by
gspirito
▴ 10
1
vote
0
replies
768
views
ComBat before or after filtering
ComBat
batchadjustment
microarray
4.5 years ago by
averagelife
▴ 10
1
vote
5
replies
1.9k
views
Using np to target subsampling
nonpareil
coassembly
metagenomics
updated 4.5 years ago by
h.mon
35k • written 4.6 years ago by
andrew
▴ 10
1
vote
2
replies
1.5k
views
Picard LiftoverVcf warning - input malformated
vcf
picard
warning
error
liftover
4.5 years ago by
Yuri
• 0
2
votes
2
replies
1.3k
views
Forum:
reporting differentially expressed genes in a global RNA-seq study
DESeq2
RNA-seq
expression
heatmaps
transcriptomics
4.5 years ago by
thomas.welch
▴ 50
0
votes
3
replies
2.9k
views
Installing stringr after upgrading from Ubuntu 18.04 to 20.04
18.04
20.04
stringr
require
error
updated 4.5 years ago by
Jean-Karim Heriche
27k • written 4.5 years ago by
tul66893
• 0
1
vote
4
replies
1.5k
views
WGCNA -RNAseq data- strong correlation with TIN
WGCNA
TIN
RNAsequencing
updated 4.5 years ago by
cera.fisher
▴ 10 • written 4.6 years ago by
Geor
• 0
1
vote
5
replies
2.5k
views
Unable to download R package
BiocManager
updated 4.5 years ago by
GenoMax
154k • written 4.5 years ago by
Kira
• 0
0
votes
0
replies
734
views
Is there a limit on the number of query in cir_query()?
R
SMILES
webchem
4.5 years ago by
Arindam Ghosh
▴ 550
2
votes
8
replies
5.0k
views
How to produce a heatmap by keeping the original data and a log color scale?
R
heatmap
ggplot2
visualization
updated 4.5 years ago by
cpad0112
21k • written 4.5 years ago by
anikcropscience
▴ 270
0
votes
0
replies
1.4k
views
Memory issue with my PC when trying to convert PLINK to TreeMix
STACKS
bash
vcf
plink
treemix
4.5 years ago by
hemr3
▴ 10
0
votes
11
replies
4.1k
views
different sequencing depths for Input and IP in ChIP-Seq
depth
ChIP-Seq
sequencing
normalisation
4.5 years ago by
Genestar
• 0
0
votes
1
reply
2.4k
views
Seurat - setting random seed for FindNeighbors, FindClusters
seurat
clustree
4.5 years ago by
bsmith030465
▴ 250
1
vote
0
replies
679
views
Snakemake/Google-Life-Sciences aggregate funtion issue
snakemake
Google-Life-Sciences
4.5 years ago by
Stephan
▴ 10
6
votes
8
replies
5.9k
views
Modeling Chip-Seq Background Using Edger'S Glm Functionality?
chip-seq
edger
updated 4.5 years ago by
ATpoint
90k • written 13.3 years ago by
Ryan Thompson
★ 3.7k
0
votes
2
replies
1.1k
views
how to get the assembly number of an array with a script
ncbi
4.5 years ago by
Debut
▴ 20
0
votes
2
replies
1.9k
views
How exactly does diffBind count reads?
atac-seq
diffbind
updated 2.5 years ago by
Ram
45k • written 4.6 years ago by
iamjli
▴ 10
1
vote
1
reply
3.1k
views
Diffbind fold difference calculation
diffbind
normalization
fold
updated 4.5 years ago by
Rory Stark
★ 2.2k • written 4.6 years ago by
Amy
• 0
4
votes
10
replies
3.5k
views
Beagple 5.2 phasing error
vcf
beagle
plink
phasing
updated 4.3 years ago by
4galaxy77
2.9k • written 4.6 years ago by
pmc.sa
▴ 40
2
votes
2
replies
2.3k
views
Understanding PCA plot from DiffBind
diffbind
pca
chip-seq
updated 4.5 years ago by
Rory Stark
★ 2.2k • written 4.6 years ago by
Marco Pannone
▴ 810
0
votes
1
reply
1.7k
views
Error executing process > 'read_clustering (1)' In NanoCLUST
NanoporeSequencing
16srrna
NanoClust
updated 4.5 years ago by
Carambakaracho
★ 3.3k • written 4.5 years ago by
twinklemishra0892
▴ 10
0
votes
3
replies
1.5k
views
i need help mouse prostata single cell data
scRNAseq
porstate
mouse
updated 4.5 years ago by
h.mon
35k • written 4.5 years ago by
rodriguezcruz0010
• 0
1
vote
4
replies
2.6k
views
How to plot chipseq peak relative to TSS for some genes ?
chipseq
R
plotwithR
TSS
peak
updated 4.5 years ago by
Carambakaracho
★ 3.3k • written 4.5 years ago by
Sarah
▴ 10
0
votes
0
replies
656
views
Transforming a straight image #1 into bent/curved form and align with bent/curved image #2.
image
bent
imageprocessing
transform
align
4.5 years ago by
karolina.kowalska9696
• 0
122,200 results • Page
661 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: 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…
Comment: ID unifiying across different datasets
by
GenoMax
154k
You can use the [**ID mapping tool**][1] from UniProt site (third ID did not map from the list above): From To P68104 ENSG0000015…
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