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178 results • Page
2 of 4
Sort: Views
Rank
Views
Votes
Replies
3
votes
4
replies
358
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm
ChIP-seq
consensus
peaks
2 days ago by
Alexandra
• 0
3
votes
6
replies
357
views
Problem in getting geo file through GEOQUERY
geoquery
Geo
updated 5 days ago by
Ram
44k • written 6 days ago by
anasjamshed
▴ 120
0
votes
4
replies
344
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
6 days ago by
Luqman
• 0
4
votes
6
replies
343
views
Error with BiocParallel. No barcodes files found
Barcodes
scRNA-seq
SingleCellExperiment
4 days ago by
bio_info
▴ 20
2
votes
2
replies
331
views
Annotating single cell data automatically
single-cell
updated 10 hours ago by
Nat.Nataren
▴ 20 • written 5 weeks ago by
Gerard
• 0
2
votes
6
replies
332
views
How to get the ratio of allele counts from GATK derived VCF file?
Freebayes
GATK
SNP
VCF
5 days ago by
anikcropscience
▴ 230
1
vote
3
replies
329
views
Filtering VCF files based on VAF giving incorrect results
GATK
picard
VCF
bcftools
updated 6 days ago by
Ram
44k • written 13 days ago by
Arton
▴ 10
1
vote
4
replies
329
views
Single cell analysis: Unable to subset cells in seurat object using desired nFeature_RNA cut off
single-cell
4 days ago by
sc_analysis
• 0
1
vote
3
replies
328
views
Error when looping over multiple columns in a data frame in R
Statistics
R
updated 4 days ago by
Jeremy
▴ 910 • written 5 days ago by
Mohamed Samir
▴ 30
1
vote
2
replies
322
views
Error when i use EVidenceModeler to do the genome annotation
EVidenceModeler
annotation
genome
3 days ago by
peanut
• 0
2
votes
3
replies
318
views
How do we do quantification using stringtie merge option for all the merged samples generated.
stringtie
quantification
1 day ago by
Varsha
• 0
1
vote
8
replies
310
views
Error with pheatmap - 'from' must be a finite number
pheatmap
r
deseq2
updated 2 hours ago by
SamGG
▴ 20 • written 19 hours ago by
vmpsb
• 0
0
votes
3
replies
306
views
Kraken2 Custom Database non-deterministic results
Metagenomics
kraken2
updated 6 days ago by
colindaven
6.4k • written 7 days ago by
Bjorn
• 0
1
vote
3
replies
301
views
How to calculate cell type frequency between two groups in single cell data
Seurat
single-cell
sc-RNA
cell-type
updated 3 days ago by
Bastien Hervé
5.3k • written 4 days ago by
Sara
▴ 30
1
vote
3
replies
300
views
Failed to download data from EBI with ascp
EBI
aspera
updated 10 hours ago by
jude
• 0 • written 6 weeks ago by
biock
▴ 60
0
votes
4
replies
299
views
How to add Ensembl ids after Pseudobulk analysis by DESeq2
Seurat
Pseudobulk
single-cell
DESeq2
scRNA
updated 3 hours ago by
jared.andrews07
★ 17k • written 2 days ago by
Sara
▴ 30
0
votes
6
replies
295
views
from CRAM to fastq
FASTQ
WGS
CRAM
updated 5 days ago by
ATpoint
82k • written 6 days ago by
machaalani29
• 0
1
vote
4
replies
292
views
Genotyping sites with N in reference genome
GATK
UnifiedGenotyper
6 days ago by
shpak.max
▴ 50
1
vote
2
replies
285
views
Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLINK's logistic regression analysis and covariates
PLINK
GWAS
SNP
4 days ago by
F110152169
• 0
2
votes
4
replies
283
views
Allele count of 2 for homoplasmic MT variants in VCF
Variant-Calling
GATK
VCF
5 days ago by
Arton
▴ 10
0
votes
1
reply
272
views
GWAS Phenotypes
GWAS
updated 5 days ago by
韩雨
• 0 • written 6 weeks ago by
solomoncharles77
▴ 90
2
votes
3
replies
270
views
How to calculate nucleotide diversity (mtDNA, PacBio_data), Suggest me some tools
NucleotideDiversity
mtDNA
PacBio
4 days ago by
hashim.rana11
▴ 20
0
votes
5
replies
268
views
Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files
Bowtie
4 days ago by
Deepthi
• 0
0
votes
3
replies
256
views
z-score of gene set
z-score
scRNA
gene-set
6 days ago by
Hien
• 0
4
votes
2
replies
251
views
Number of non-ATCG nucleotides replaced by Salmon
rna-seq
stringtie
salmon
updated 15 hours ago by
Ram
44k • written 3 days ago by
Tonya S.
▴ 10
0
votes
2
replies
251
views
What do the transcript variant # mean in RefSeq?
refseq
updated 4 days ago by
Ram
44k • written 5 days ago by
curious
▴ 750
1
vote
2
replies
249
views
Construction of circos plot from WGS data
WGS
Circos
4 days ago by
Anitha
▴ 10
0
votes
4
replies
248
views
Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
GATK
UnifiedGenotyper
6 days ago by
shpak.max
▴ 50
1
vote
2
replies
246
views
Setting a threshold on gene expression for subsetting (scRNA-seq)
scRNA-seq
updated 2 days ago by
LauferVA
4.2k • written 3 days ago by
carolofharvest
▴ 40
0
votes
2
replies
244
views
Tools for chromosomal aneuploidy detection
genetics
aneuploidy
NGS
human
updated 1 day ago by
a.alnawfal.1992
▴ 260 • written 5 days ago by
adarsh_pp
▴ 40
1
vote
3
replies
244
views
Trimmomatic running but files containing purged reads are empty
fastqc
fastq
trimmomatic
updated 6 days ago by
GenoMax
142k • written 6 days ago by
Wilber0x
▴ 50
0
votes
2
replies
241
views
perl Error - needLargeMem Bigwig
Bigwig
perl
mitosalt
1 day ago by
marco.barr
▴ 130
4
votes
1
reply
240
views
PCA plot no distinct cluster. Only p < 0.05 indicates significant DEGs, while adj p < 0.05 does not.
RNA-seq
padj
p-value
updated 4 days ago by
swbarnes2
14k • written 5 days ago by
May Ling
• 0
3
votes
3
replies
237
views
Unexpected read length from NGS
NGS
Illumina
4 days ago by
QX
• 0
0
votes
2
replies
235
views
How to decrease the motif score?
scores
Motif
updated 8 hours ago by
dthorbur
★ 2.0k • written 3 days ago by
Hadia
• 0
0
votes
4
replies
231
views
merge overlaps and remove non overlap genomic windows
BED
intersection
overlap
5 days ago by
reza
▴ 300
2
votes
0
replies
227
views
Job:
Permanent Position as Researcher/Computational Biologist at the National Genomics Infrastructure (Sweden)
Genomics
Sequencing
Sweden
Stockholm
SciLifeLab
5 days ago by
Matthias Zepper
4.6k
3
votes
4
replies
226
views
Invalid CIGAR after using bam clipOverlap
validatesamfile
cigar
bam
clipoverlap
1 day ago by
MboiTui
▴ 20
0
votes
3
replies
224
views
Splitting query fasta file for Diamond Blastp make the process faster?
DIAMOND
4 days ago by
kmat
• 0
2
votes
3
replies
219
views
Search within posts based on tags using the Biostars API
api
meta
updated 3 hours ago by
Ram
44k • written 1 day ago by
Bálint
▴ 10
3
votes
2
replies
218
views
converting transcript IDs (Ensembl) to gene symbols in R
RNA-seq
updated 6 days ago by
GenoMax
142k • written 7 days ago by
ashkan
▴ 160
2
votes
1
reply
217
views
Why some SNP's allele frequencies in gnomAD are so different between v2 and v4?
AF
gnomAD
SNP
updated 4 days ago by
Jeremy Leipzig
22k • written 4 days ago by
liaotsungjen
▴ 10
5
votes
3
replies
216
views
FastQC interpretation - 16S sequencing
interpretation
amplicon
Fastqc
16S
updated 6 days ago by
GenoMax
142k • written 6 days ago by
Christopher
▴ 10
1
vote
3
replies
211
views
Question about samtools view flags (paired reads vs. properly paired reads)
samtools
updated 6 days ago by
Pierre Lindenbaum
162k • written 7 days ago by
mrk
• 0
3
votes
2
replies
211
views
vg autoindex seems stuck after a week of running
vg
pangenome
10 hours ago by
StevieP
▴ 10
1
vote
3
replies
210
views
downloading chemical database from ChEMBL
ChEMBL
PyRMD
Virtual-Screening
updated 6 days ago by
GenoMax
142k • written 6 days ago by
s
• 0
0
votes
1
reply
209
views
Overlapping clusters for different biological conditions: Seurat, UMAP
Seurat
scRNA-seq
UMAP
updated 4 days ago by
Bastien Hervé
5.3k • written 4 days ago by
bio_info
▴ 20
0
votes
1
reply
205
views
BAM to Bedgraph creating an empty file
Bisulfite-seq
bismark
updated 1 day ago by
raphael.B
▴ 520 • written 4 days ago by
irebekah.c
• 0
0
votes
0
replies
203
views
Job:
2 PhD Students in single-cell bioinformatics
PhD
Genomics
single-cell
NGS
4 days ago by
mtabaka
• 0
2
votes
2
replies
197
views
Help me with Heatmap
RNA-seq
R
DESeq2
updated 8 hours ago by
zx8754
11k • written 1 day ago by
vmpsb
• 0
178 results • Page
2 of 4
Recent Votes
Comment: Is there any minimum number of counts in scRNAseq to consider that a gene is exp
Comment: Best practices in Fungal Genome Assembly
Answer: Best practices in Fungal Genome Assembly
Comment: Best practices in Fungal Genome Assembly
Answer: UMI-Tools knee-method has great influence on the results of white list
Answer: UMI-Tools knee-method has great influence on the results of white list
linkage disequilibrium analysis
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Recent Replies
Comment: I cannot download VG in any way
by
Ram
44k
In that case, OP should have said "Cannot install SequenceTube", since that is the problem, not vg. Maybe this is the SequenceTube that OP…
Comment: I cannot download VG in any way
by
GenoMax
142k
I read that to mean that the only way they were able to download `vg` was by using `conda`. Since `SequenceTube` (whatever that is) require…
Comment: I cannot download VG in any way
by
Ram
44k
> The only way that I managed to download vg is using conda, however since my primary goal is to download SequenceTube You're mentioning t…
Comment: I cannot download VG in any way
by
Ram
44k
Also, OP buries the lede and uses a misleading title. They are able to install vg using conda, but that is secondary to them using a differ…
Comment: Can I count UMI-barcode combination without mapping?
by
GenoMax
142k
You can use some code I have here for inspiration: https://www.biostars.org/p/270737/#270753 You can extract the UMI by using. $ awk…
Comment: Best practices in Fungal Genome Assembly
by
samuel.a.odonnell
▴ 540
I think 10 rounds in excessive. I usually only run 1-3 rounds (as long-read accuracy has improved I have used fewer and fewer rounds), but …
Comment: I cannot download VG in any way
by
GenoMax
142k
Why are you not downloading the `vg` binaries provided here: https://github.com/vgteam/vg/releases/tag/v1.57.0 Use the `Click here to Downl…
Comment: Best practices in Fungal Genome Assembly
by
Umer
▴ 50
Hi, Thanks for your suggestions. > polish the long-read assembly afterwards Previously, I used Pilon for polishing and i did 10 rounds. (…
Comment: How do I check if a DNA sequence of a gene is supported by RNAseq data?
by
Jack
• 0
I have the DNA sequences of every phase variable locus in the genomes of 8 bacterial isolates. Repeats range from polyG tracts around 9-20…
Comment: Best practices in Fungal Genome Assembly
by
samuel.a.odonnell
▴ 540
For the short-read strains: <br/> I would recommend just using SPADES For the strains with long-reads: <br/> I think spades and masurca as…
Comment: txt file to bigwig
by
GenoMax
142k
Click on `edit`. That should open the edit window which will have a `Delete` button at bottom right to delete the comment/reply.
Comment: UMI-Tools knee-method has great influence on the results of white list
by
Assa Yeroslaviz
★ 1.9k
Can you pls make it an answer so that I can accept it? thx
Comment: Best practices in Fungal Genome Assembly
by
samuel.a.odonnell
▴ 540
I think tools like quickmerge (or Ragtag's patch command) can help for long-read assemblies, but I would definitely avoid using them with s…
Comment: txt file to bigwig
by
sogand
• 0
Hi, I tried to delete my comment but can't see any delete/remove option here! Thanks
Comment: Error with pheatmap - 'from' must be a finite number
by
Ram
44k
You'd see a different issue if the vector being analyzed contained character entries. This is clearly a problem with NA/NaN/Inf values in t…
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