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168 results • Page
2 of 4
Sort: Views
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Views
Votes
Replies
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
336
views
Annotating single cell data automatically
single-cell
updated 13 hours ago by
Nat.Nataren
▴ 20 • written 5 weeks ago by
Gerard
• 0
2
votes
6
replies
333
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
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
329
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
8
replies
326
views
Error with pheatmap - 'from' must be a finite number
pheatmap
r
deseq2
updated 5 hours ago by
SamGG
▴ 20 • written 21 hours ago by
vmpsb
• 0
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
0
votes
4
replies
306
views
How to add Ensembl ids after Pseudobulk analysis by DESeq2
Seurat
Pseudobulk
single-cell
DESeq2
scRNA
updated 5 hours ago by
jared.andrews07
★ 17k • written 3 days ago by
Sara
▴ 30
0
votes
3
replies
307
views
Kraken2 Custom Database non-deterministic results
Metagenomics
kraken2
updated 6 days ago by
colindaven
6.4k • written 8 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 13 hours ago by
jude
• 0 • written 6 weeks ago by
biock
▴ 60
0
votes
6
replies
297
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
287
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
284
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
271
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
252
views
Number of non-ATCG nucleotides replaced by Salmon
rna-seq
stringtie
salmon
updated 18 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 5 days ago by
Ram
44k • written 5 days ago by
curious
▴ 750
0
votes
2
replies
250
views
Tools for chromosomal aneuploidy detection
human-genetics
aneuploidy
NGS
updated 2 hours ago by
Ram
44k • written 5 days ago by
adarsh_pp
▴ 40
1
vote
2
replies
250
views
Construction of circos plot from WGS data
WGS
Circos
4 days ago by
Anitha
▴ 10
1
vote
2
replies
249
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
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
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
0
votes
2
replies
241
views
How to decrease the motif score?
Motif-score
updated 40 minutes ago by
Ram
44k • written 3 days ago by
Hadia
• 0
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 5 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
4
replies
231
views
merge overlaps and remove non overlap genomic windows
BED
intersection
overlap
5 days ago by
reza
▴ 300
3
votes
4
replies
230
views
Invalid CIGAR after using bam clipOverlap
validatesamfile
cigar
bam
clipoverlap
1 day ago by
MboiTui
▴ 20
2
votes
0
replies
229
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
2
votes
3
replies
226
views
Search within posts based on tags using the Biostars API
api
meta
updated 5 hours ago by
Ram
44k • written 1 day ago by
Bálint
▴ 10
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
1
reply
219
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
3
votes
2
replies
219
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
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
3
votes
2
replies
212
views
vg autoindex seems stuck after a week of running
vg
pangenome
13 hours ago by
StevieP
▴ 10
1
vote
3
replies
211
views
downloading chemical database from ChEMBL
ChEMBL
PyRMD
Virtual-Screening
updated 6 days ago by
GenoMax
142k • written 7 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
206
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
2
votes
2
replies
204
views
Help me with Heatmap
RNA-seq
R
DESeq2
updated 11 hours ago by
zx8754
11k • written 1 day ago by
vmpsb
• 0
0
votes
0
replies
204
views
Job:
2 PhD Students in single-cell bioinformatics
PhD
Genomics
single-cell
NGS
4 days ago by
mtabaka
• 0
0
votes
1
reply
198
views
Trying to understand warning from MACS2 about too few paired peaks and differing results in DiffBind
MACS2
ATACseq
DiffBind
updated 5 days ago by
jared.andrews07
★ 17k • written 5 days ago by
atan
• 0
0
votes
2
replies
197
views
vcf phasing
beagle
WhatsHap
phasing
6 days ago by
safeassli
▴ 10
3
votes
2
replies
192
views
Multiplexing for pooled CRISPR screen sequencing
multiplex
CRISPR-screen
Illumina
6 days ago by
Tuấn Anh
• 0
0
votes
2
replies
190
views
CreateSeuratObject taking very long
seurat
4 days ago by
eae6d2e7
• 0
0
votes
1
reply
189
views
Does prokka work the same on forward and reverse complementary reads?
Prokka
updated 4 days ago by
Pierre Lindenbaum
162k • written 4 days ago by
Maksim
• 0
168 results • Page
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Recent Votes
when I use htslib to write a bam. Error of "truncated file" shows by samtools
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Answer: vg call - Selecting reference path to call on
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Comment: dbNSFP4.7a database format to Annovar Format?
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Comment: How to Convert CNV Data to CNA Format for Reproducing Results with the Padma Pac
by
Ngrin
• 0
Thanks @Zhenyu Zhang for your response. I have just looked at the files you mentioned. Do you have any recommended package or code snippet …
Comment: coding and non-coding region of the viral genome
by
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• 0
As far I understand non coding region equal to the intergenic region? please can you write an example for how to calculate one region ? I…
Comment: when I use htslib to write a bam. Error of "truncated file" shows by samtools
by
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162k
Thanks for the code, it's interesting. It doesn't solve the problem , but the code is missing `#include <htslib/bgzf.h>` and I cannot fin…
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In the GDC, there are raw float value CNV data, and integer CNV values after advanced modeling. If you only want those floating-point numbe…
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by
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44k
Please edit your original post and add this at the top so everyone reads that first. GeneCards politely asks people not to scrape - not res…
Comment: I cannot download VG in any way
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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…
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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…
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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…
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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…
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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…
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Hi, Thanks for your suggestions. > polish the long-read assembly afterwards Previously, I used Pilon for polishing and i did 10 rounds. (…
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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…
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