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122,202 results • Page
685 of 2445
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Rank
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Votes
Replies
8
votes
4
replies
4.6k
views
Any standalone tool for INDEL Realignment?
indels
deepvariant
realignment
updated 4.6 years ago by
ATpoint
90k • written 4.6 years ago by
NikhilP
▴ 20
5
votes
4
replies
1.9k
views
Complete of Illumina raw reads
assembly
illumina
4.6 years ago by
A_heath
▴ 180
0
votes
2
replies
1.1k
views
Jellyfish databases overlap
Jellyfish
4.6 years ago by
MarVi
▴ 30
0
votes
0
replies
842
views
How to add rs ID to SNP dosage file
SNPs
Plink
rsID
updated 4.6 years ago by
Pierre Lindenbaum
166k • written 4.6 years ago by
salman_96
▴ 70
0
votes
0
replies
713
views
Validation of Bioinformatics pipeline with NA12763
hap.py
updated 2.7 years ago by
Ram
45k • written 4.6 years ago by
esimonova.me
▴ 30
9
votes
6
replies
4.9k
views
Why does Illumina have the extra +1 cycle?
NGS
Illumina
updated 4.6 years ago by
GenoMax
154k • written 4.6 years ago by
Michael
▴ 290
1
vote
4
replies
1.6k
views
How to find the true orthologs from recipocal blast hits (blastn) ?
RNA
DNA
blast
alignment
3.4 years ago by
sunnykevin97
▴ 1000
0
votes
2
replies
901
views
Phylotranscriptomics approach understanding evolution from museum specimens ?
genomics
RNA
alignment
4.6 years ago by
sunnykevin97
▴ 1000
0
votes
2
replies
1.7k
views
R ggplot2 creating separate plots for different subsets of rows
r
facet-wrap
cowplot
for-loop
ggplot2
4.6 years ago by
moritz.lasse
• 0
2
votes
2
replies
1.9k
views
TiTv ratio
TiTv
QC
stat
WES
BCFtools
updated 4.6 years ago by
prasundutta87
▴ 730 • written 4.6 years ago by
DKA
▴ 40
3
votes
5
replies
6.3k
views
How to explain fastq insert size peak
RNAseq
trimming
updated 4.6 years ago by
GenoMax
154k • written 4.6 years ago by
Michael
▴ 290
0
votes
0
replies
913
views
News:
Online training - Network Analysis in R
R
NetworkAnalysis
4.6 years ago by
Physalia-courses
★ 2.7k
0
votes
1
reply
1.7k
views
Convert a DNA sequence to MEME format
FIMO
fasta
motif
MEME-suite
format
conversion
updated 4.6 years ago by
GenoMax
154k • written 4.6 years ago by
tianshenbio
▴ 190
5
votes
5
replies
3.6k
views
Trying to do log2 transformation of my rna seq data
R
updated 4.6 years ago by
Gordon Smyth
★ 8.6k • written 4.6 years ago by
rishav513
▴ 30
1
vote
0
replies
1.1k
views
rvtest fails after Snpeff annotation: Core dumped error
snpeff
Genomics
rvtests
4.6 years ago by
raphael.B
▴ 540
1
vote
7
replies
2.9k
views
What's the most efficient way to load k-mers into dict in python?
K-mer
updated 4.4 years ago by
Ram
45k • written 4.6 years ago by
Ray
• 0
1
vote
0
replies
1.2k
views
Job:
Computational Genomics Position is Opening at Johnson & Johnson
genetics
statistical
genomics
updated 2.5 years ago by
Ram
45k • written 4.6 years ago by
Shicheng Guo
★ 9.6k
0
votes
2
replies
2.1k
views
Structural variations (SV calling using Parliament2)
SV
CNV
software error
updated 4.6 years ago by
GenoMax
154k • written 5.3 years ago by
Nitha
▴ 20
1
vote
3
replies
1.6k
views
how to add scientific samples to yfull
samples
yfull
updated 4.6 years ago by
natevkup
• 0 • written 4.6 years ago by
Dex
• 0
0
votes
0
replies
877
views
ChIPSeq and WGBS Read mapping to HLA region
WGBS
MHC-1
ChIPSeq
bisulfite
hla
4.6 years ago by
Nikleotide
▴ 130
2
votes
3
replies
3.3k
views
hmmer e-value
hmmer
pfam
updated 4.6 years ago by
Mensur Dlakic
★ 30k • written 4.6 years ago by
CHINMAYA
▴ 10
0
votes
0
replies
799
views
Job:
Postdoctoral Research Scholar with ASU and Sun Genomics - human gut microbiome and Autism
biodesign
biotech
autism
microbiome
postdoc
4.6 years ago by
Leah
• 0
3
votes
1
reply
1.1k
views
How to download specific genomes
comparative
ncbi
genomes
genomics
assembly
updated 4.6 years ago by
GenoMax
154k • written 4.6 years ago by
vm.higareda
▴ 30
0
votes
3
replies
2.5k
views
Network X used in Biopython
Biopython
Graphs
Python
4.6 years ago by
anasjamshed
▴ 140
8
votes
6
replies
2.7k
views
How to select genes with multi-exon 3'UTR
rna-seq
genome
gff
gene
updated 4.6 years ago by
Juke34
9.3k • written 4.7 years ago by
tianshenbio
▴ 190
1
vote
3
replies
1.2k
views
How to get DNA and RNA datasets from GEO,TCGA and EBI
dna-seq
Genome
rna-seq
4.6 years ago by
Milan
• 0
2
votes
2
replies
1.8k
views
How does e value for diamond blastx affects the result
analysis
metagenomics
genomics
data
4.6 years ago by
serene.s
• 0
2
votes
1
reply
2.1k
views
Picard and GaTK HaplotypeCaller
gatk
picard
haplotypecaller
duplicates
updated 4.6 years ago by
prasundutta87
▴ 730 • written 4.6 years ago by
Afzal
• 0
0
votes
3
replies
1.7k
views
Generating an MDS plot in R for population stratification
R
MDS
Stratification
PCA
PLINK
4.6 years ago by
nliberman
• 0
3
votes
2
replies
6.0k
views
How to install PEER in R?
PEER
R
Rstudio
RNA-Seq
4.6 years ago by
sahar.salimi92
• 0
9
votes
5
replies
5.5k
views
tool for bam soft clipping reads within bed file regions
bam
clipping
bed
updated 3.4 years ago by
Ram
45k • written 9.8 years ago by
14134125465346445
★ 3.6k
13
votes
14
replies
9.4k
views
8 follow
Limiting variant calls to amplicon target regions?
trimming
alignment
updated 2.9 years ago by
Ram
45k • written 10.4 years ago by
drollix
▴ 10
1
vote
7
replies
4.6k
views
How to merge and average BedGraph files
bedtools
terminal
bg
bedgraph
4.6 years ago by
a_bis
▴ 40
2
votes
1
reply
1.0k
views
Tool:
Bioinformatics Programming Package
Package
updated 2.5 years ago by
Ram
45k • written 4.6 years ago by
Asad Bilal
▴ 10
0
votes
2
replies
1.4k
views
Can someone help me understand map and hap files
admixsim
hap
map
updated 2.7 years ago by
Ram
45k • written 4.6 years ago by
brunomiwa
• 0
0
votes
0
replies
1.4k
views
barplot for enrichment results
clusterProfile
barplot
RNAseq
DESeq2
updated 4.6 years ago by
GenoMax
154k • written 4.6 years ago by
giuly.lg.95
• 0
2
votes
6
replies
2.3k
views
How can I retrieve nucleotide sequences from amino acid sequences?
nucleotide
sequences
protein
updated 4.6 years ago by
lieven.sterck
16k • written 4.6 years ago by
Rui
▴ 50
0
votes
3
replies
1.1k
views
Package to predict genomic variants from rna-seq read data
Genomics
rna-seq
4.6 years ago by
dk0319
▴ 70
0
votes
1
reply
1.7k
views
Running Snakemake on the computing cluster
Snakemake
HPC
updated 4.6 years ago by
Ram
45k • written 4.6 years ago by
wangdp123
▴ 340
0
votes
0
replies
877
views
Big difference in "free parameter" (np) in Sites Models for different models with CODEML (PAML)
Site-Models
sequence
PAML
evolution
CODEML
4.6 years ago by
mauricio.1313
• 0
0
votes
1
reply
3.0k
views
use 16s rRNA data to predict metabolic pathway according to genome-scale network reconstructions
genome
reconstruction
metabolic
updated 4.6 years ago by
fabricio.motteran
• 0 • written 8.2 years ago by
fanglujing
▴ 60
1
vote
1
reply
1.4k
views
Extract MAF for vcf file
vcf
MAF
updated 4.6 years ago by
Pierre Lindenbaum
166k • written 4.6 years ago by
Sumeet
▴ 10
3
votes
3
replies
1.5k
views
filtering a dataframe of DE GO terms with a dataframe containing GO terms of interest
GeneOntology
4.6 years ago by
peter.berry5
▴ 60
3
votes
2
replies
5.1k
views
How to fix error in Entrez-Direct: 429 Too Many Requests
Entrez-Direct
updated 22 months ago by
Ram
45k • written 4.6 years ago by
f-rasmussen
▴ 10
1
vote
2
replies
1.2k
views
SNP/Gene to cell type
cell
SNPs
updated 2.5 years ago by
Ram
45k • written 4.6 years ago by
salman_96
▴ 70
4
votes
2
replies
1.6k
views
Do FASTQ files from ArrayExpress already have adapter sequences trimmed?
adapters
ArrayExpress
updated 4.6 years ago by
GenoMax
154k • written 4.6 years ago by
Stevens
▴ 30
0
votes
3
replies
1.7k
views
Different files with SRA Explorer and SRA toolkit fasterq-dump
SRA_Explorer
SRA-toolkit
updated 4.6 years ago by
GenoMax
154k • written 4.6 years ago by
Rogerio Ribeiro
▴ 110
0
votes
1
reply
1.2k
views
driver genes per sample or per group?
driver
genes
updated 2.7 years ago by
rohitsatyam102
▴ 940 • written 4.6 years ago by
whb
▴ 60
45
votes
23
replies
7.7k
views
6 follow
Forum:
biostar.slack.com: Chat for the biostars community -- [ feel free to join ]
chat
slack
updated 2.8 years ago by
Ram
45k • written 7.7 years ago by
Devon Ryan
105k
0
votes
0
replies
1.2k
views
Interpretation of CNVkit output
gainloss
tumor
InterpretationOfResults
CNVkit
4.6 years ago by
Samiah
▴ 10
122,202 results • Page
685 of 2445
Recent Votes
what cause poly-G from NextSeq
what cause poly-G from NextSeq
A: what cause poly-G from NextSeq
A: what cause poly-G from NextSeq
How to trim transcripts using information from NCBI contamination screen report
How to trim transcripts using information from NCBI contamination screen report
Trimming sequences based on NCBI contamination screen report
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★ 4.4k
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Biomed-jeh
▴ 70
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gernophil
▴ 130
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Recent Replies
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 !
Comment: 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…
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…
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