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677 results • Page
3 of 14
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Votes
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3
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3
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278
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getting exon coordinates
genomics
updated 10 days ago by
Ram
44k • written 11 days ago by
Xbox_27
• 0
3
votes
4
replies
374
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq
patch
freeze
genome
updated 9 days ago by
Jeremy Leipzig
22k • written 11 days ago by
Ali
• 0
3
votes
4
replies
6.3k
views
MAUVE: No gene annotations in Genbank file alignments
software-error
MAUVE
RAST
genbank
alignment
updated 4 days ago by
pramach1
▴ 40 • written 9.8 years ago by
tptacek3050
▴ 70
3
votes
0
replies
1.1k
views
Tool:
Sars-Cov-2 Genome & ACE 2 Exploration
sequence
alignment
SNP
genome
22 days ago by
Ibrahim Tanyalcin
★ 1.2k
3
votes
8
replies
665
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
20 days ago by
Qroid
▴ 40
3
votes
3
replies
392
views
Is it possible to bulk download files from GEO repository?
RNA-seq
Galaxy
Tanscriptomics
updated 27 days ago by
noodle
▴ 590 • written 28 days ago by
WUSCHEL
▴ 760
3
votes
1
reply
235
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair
samtools
alignment
updated 14 days ago by
aw7
▴ 310 • written 18 days ago by
Zeng Hao
▴ 40
3
votes
2
replies
442
views
Extract protein sequence
fasta
alignment
blast
26 days ago by
anna
▴ 20
3
votes
4
replies
510
views
Design matrix Differential expression analysis
RNA-seq
Differential-expression
updated 20 days ago by
Gordon Smyth
★ 7.2k • written 23 days ago by
SHN
▴ 40
3
votes
5
replies
453
views
Super ehancers
enhancers
updated 5 days ago by
jared.andrews07
★ 17k • written 25 days ago by
Oburah
• 0
3
votes
3
replies
400
views
What analysis suitable to identify similarly expressed genes between two samples (treated vs untreated). Contrary to DGE analysis,
Gene-Expression
RNA
NOISeq
DGE
updated 24 days ago by
ATpoint
82k • written 25 days ago by
alifafiq1
• 0
3
votes
2
replies
181
views
How to interpret this plotMDS of three disease clusters?
microarray
plotMDS
DEGs
updated 4 days ago by
ATpoint
82k • written 4 days ago by
egascon
• 0
3
votes
6
replies
554
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 14 days ago by
Pine
▴ 20 • written 21 days ago by
snajafy
• 0
3
votes
3
replies
307
views
what is another word for a BLAST "hit"?
blast
alignment
16 days ago by
dec986
▴ 380
3
votes
4
replies
4.0k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 19 days ago by
chloek88
• 0 • written 5.6 years ago by
Philipp Bayer
8.5k
3
votes
8
replies
6.7k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 24 days ago by
Sd
• 0 • written 5.2 years ago by
Nicolas Rosewick
11k
3
votes
4
replies
160
views
Invalid CIGAR after using bam clipOverlap
validatesamfile
cigar
bam
clipoverlap
5 hours ago by
MboiTui
▴ 20
2
votes
5
replies
2.6k
views
identifying transgene insertion site in WGS
WGS
insertion site
trangene
de-novo
soap
updated 18 days ago by
Cameron.walker9900
• 0 • written 5.1 years ago by
Assa Yeroslaviz
★ 1.8k
2
votes
1
reply
368
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
updated 23 days ago by
chrchang523
10k • written 27 days ago by
8armed
▴ 10
2
votes
3
replies
299
views
Finding variants within a subset of a BAM file
variant
calling
12 days ago by
ramiro.barrantes
• 0
2
votes
4
replies
337
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
12 days ago by
Esraa
• 0
2
votes
1
reply
147
views
What is the bin size for Bamcompare?
chip-seq
deeptools
bamcompare
updated 12 days ago by
Ram
44k • written 13 days ago by
Emily
▴ 20
2
votes
4
replies
262
views
Help with IGV abbreviation
igv
updated 12 days ago by
Ram
44k • written 13 days ago by
GeneC
• 0
2
votes
11
replies
745
views
ComplexHeatmap - How to change fontsize of rowAnnotation
r
ComplexHeatmap
updated 22 hours ago by
Ram
44k • written 9 days ago by
hannes.bongartz
• 0
2
votes
0
replies
214
views
Job:
Permanent Position as Researcher/Computational Biologist at the National Genomics Infrastructure (Sweden)
Genomics
Sequencing
Sweden
Stockholm
SciLifeLab
3 days ago by
Matthias Zepper
4.6k
2
votes
3
replies
255
views
How to calculate nucleotide diversity (mtDNA, PacBio_data), Suggest me some tools
NucleotideDiversity
mtDNA
PacBio
3 days ago by
hashim.rana11
▴ 20
2
votes
3
replies
895
views
Issues with Mixture file when using CIBERSORTx
Deconvolution
CIBERSORTx
updated 22 days ago by
vjanve
• 0 • written 7 months ago by
mateomejias
• 0
2
votes
7
replies
1.4k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq
Salmon
Isoseq
updated 28 days ago by
Gordon Smyth
★ 7.2k • written 9 months ago by
Calum
▴ 10
2
votes
0
replies
160
views
Herald:
The Biostar Herald for Monday, May 13, 2024
herald
13 days ago by
Biostar
2.8k
2
votes
4
replies
319
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell
seurat
10XGenomics
scRNAseq
updated 11 days ago by
yura.grabovska
▴ 90 • written 11 days ago by
ev97
▴ 20
2
votes
6
replies
437
views
BWA alignment
Samtools
bam
updated 12 days ago by
a.alnawfal.1992
▴ 260 • written 14 days ago by
Vahid
• 0
2
votes
7
replies
609
views
KEGG analysis in R
KEGG
clusterProfiler
Zea-mays
updated 5 days ago by
letizia.ottaviani
• 0 • written 6 weeks ago by
sansan_96
▴ 90
2
votes
2
replies
225
views
genome finishing
finishing
genome
updated 11 days ago by
nd48
▴ 30 • written 12 days ago by
trezini
• 0
2
votes
1
reply
271
views
RNAseq coverage vs depth for transcript isoform expression?
RNAseq
updated 8 days ago by
Gordon Smyth
★ 7.2k • written 9 days ago by
marineandriot
• 0
2
votes
3
replies
358
views
Trimming tool
Trimming
updated 6 days ago by
Ram
44k • written 9 days ago by
GeneC
• 0
2
votes
2
replies
2.7k
views
Pindel Segmentation Fault Error
pindel
updated 23 days ago by
Ruqaiya
• 0 • written 10.3 years ago by
Yuelin
▴ 20
2
votes
3
replies
387
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
updated 17 days ago by
bk11
★ 2.5k • written 22 days ago by
Yoosef
▴ 60
2
votes
3
replies
237
views
RSeQC : infer_experiment.py Error: Could not retrieve index file
RSeQC
RNA-Seq
updated 12 days ago by
Ram
44k • written 12 days ago by
Prawesh
• 0
2
votes
0
replies
173
views
News:
course on Landscape Genomics at the EPFL in Lausanne (June 17-21)
LandscapeGenomics
SNPs
LocalAdaptation
GIS
17 days ago by
carlopecoraro2
★ 2.5k
2
votes
3
replies
278
views
ggrepel function: geom_text_repel()
ggplot2
ggrepel
R
updated 10 days ago by
Ram
44k • written 11 days ago by
sooni
▴ 20
2
votes
6
replies
2.0k
views
How can you *consistently* download BioProject IDs from NCBI's BioSample database using Entrez Direct?
XML
ncbi
entrez-direct
updated 11 days ago by
Ram
44k • written 3.9 years ago by
millere
• 0
2
votes
2
replies
382
views
Association study using SNP data
Association
Allele
Parentage
SNP
21 days ago by
drajangirija
• 0
2
votes
4
replies
5.6k
views
44% Successfully Assigned Fragments with featureCounts after 85% uniquely mapped reads with STAR
rna-seq
alignment
RNA-Seq
featureCounts
STAR
updated 13 days ago by
Thind amarinder
▴ 340 • written 5.0 years ago by
garbuzov
▴ 70
2
votes
2
replies
224
views
Genome Visualization Tools
bacterial
genome
updated 12 days ago by
GenoMax
142k • written 12 days ago by
dlera.lozano
▴ 10
2
votes
4
replies
735
views
Count all variants from vcf file
variants
vcf
Count
updated 20 days ago by
Pierre Lindenbaum
162k • written 21 months ago by
t.ali
• 0
2
votes
2
replies
1.8k
views
Parametric or non-parametric tests for qPCR significance testing between treatments?
qPCR
statistical test
parametric
non-parametric
updated 23 days ago by
e.r.zakiev
▴ 210 • written 3.9 years ago by
n.anuragsharma
▴ 40
2
votes
2
replies
269
views
Raw counts using stringtie
stringtie
RNA-seq
updated 23 days ago by
GenoMax
142k • written 23 days ago by
ahmad.sajad4541
• 0
2
votes
14
replies
3.0k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 13 days ago by
Anitha
▴ 10 • written 4.9 years ago by
ww22runner
▴ 60
2
votes
9
replies
802
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 12 days ago by
Pierre Lindenbaum
162k • written 19 days ago by
schmince
• 0
2
votes
6
replies
394
views
Harmony integration group.by.var parameter
single-cell
harmony
updated 14 hours ago by
jared.andrews07
★ 17k • written 3 days ago by
Picasa
▴ 640
677 results • Page
3 of 14
Recent Votes
C: snpEff assigned all variants as modifier intergenic
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C: The Biostar Handbook. A bioinformatics e-book for beginners.
Answer: Error with BiocParallel. No barcodes files found
Error with BiocParallel. No barcodes files found
Comment: How do we do quantification using stringtie merge option for all the merged samp
Answer: bcftools view error: the tag "mis" is not defined in the VCF header
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Recent Replies
Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2
by
ATpoint
82k
Why is your `GeneName` column in mapped a mix of Ensembl IDs and gene names? What Jared wants to say is that during the preprocessing you s…
Comment: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
by
GenoMax
142k
> only give me partial results It is possible that not every Ensembl ID is going to convert to Entrez ID. Have you tried: https://www.b…
Comment: BAM to Bedgraph creating an empty file
by
raphael.B
▴ 520
You have a space in your reference path. Not sure it's intended?
Comment: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
by
Anya
• 0
Do you have any recommendations of such sources or how to search for them? I'm a newbie and I need to convert GRCh38 Ensembl IDs to Entrez …
Comment: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
by
Shred
★ 1.4k
Genecards added a footer saying that >SCRAPING AND OTHER AUTOMATED DOWNLOAD AND USE OF GENECARDS DATA STRICTLY PROHIBITED While this is …
Comment: perl Error - needLargeMem Bigwig
by
marco.barr
▴ 130
I managed to correct and solve the problem. It was due to issues with memory parameter settings on different login nodes. Additionally, I h…
Answer: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
by
Anya
• 0
Here's a slightly changed version of this script. I changed line 42 from `'title':'NCBI Entrez Gene'` to `'title':'NCBI Gene'` ). And…
Comment: How do we do quantification using stringtie merge option for all the merged samp
by
Varsha
• 0
Thank you for the detailed explanation.
Answer: How can run cd-hit-est with a clstr threshold less than 0.8?
by
Asaf
10k
For future reference The 0.8 identity threshold for EST (nucleotides) is hardcoded. However, there's an option to use `-D` (distance) in…
Answer: Tools for chromosomal aneuploidy detection
by
a.alnawfal.1992
▴ 260
As far as I know, all the tools utilised control group to compute the z score for chromosomal aneuploidy. but is your goal detect chromosom…
Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2
by
Sara
▴ 30
I used Seurat, and in Seurat, I have gene names (which some are with gene-symbols and some with ENSG ids). Then I did Pseudobulk. how can …
Comment: How to decrease the motif score?
by
ATpoint
82k
So you scan the entire genome and got nothing significant? Is that the issue?
Comment: perl Error - needLargeMem Bigwig
by
b.contreras.moreira
▴ 200
A quick search suggests the problem is your empty input file? See <https://biostar.galaxyproject.org/p/6794>
Comment: Invalid CIGAR after using bam clipOverlap
by
MboiTui
▴ 20
ooh good pickup. Might not be the problem but definitely not helping. Will re-run with streamlined workflow and with double quotes and see …
Comment: Invalid CIGAR after using bam clipOverlap
by
Pierre Lindenbaum
162k
may be not the problem but why this ` RG:Z:H7J22DRX3.${lane}-1C23074F ` in the RG. you're using single quotes with bwa-mem and it won't …
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