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351 results • Page
2 of 8
Sort: Rank
Rank
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Votes
Replies
1
vote
2
replies
226
views
BWA MEM Alignment mapped small part of the reads!!
bwa
mem
updated 1 day ago by
bioruffo
▴ 40 • written 2 days ago by
Bunit
• 0
0
votes
0
replies
106
views
Correlation analysis in single-cell sequencing data
scRNA-seq
correlation
scATAC-seq
2 days ago by
Yingying
• 0
0
votes
0
replies
103
views
MIENTURNET - miRNA enrichment analysis
miRNA-enrichment
mRNA
RNA
updated 2 days ago by
Ram
43k • written 2 days ago by
PBC
▴ 10
0
votes
3
replies
239
views
Parsing fasta file by coordinates
linux
fasta
updated 2 days ago by
GenoMax
140k • written 2 days ago by
sorrymouse
▴ 120
0
votes
2
replies
214
views
comparing VCF files
long-reads
VCF
variants
ONT
nanopore
1 day ago by
eesiribloom
▴ 50
0
votes
0
replies
84
views
Multifactor Analysis in DiffBind
DiffBind
ChIPseq
ChIP-seq
2 days ago by
erbrocato
• 0
0
votes
1
reply
127
views
Can I have multiple active GDC download tokens?
TCGA
updated 2 days ago by
GenoMax
140k • written 2 days ago by
mrk
• 0
0
votes
0
replies
101
views
How to calculate weighted transcript length for each gene?
salmon
tximport
rna-seq
updated 2 days ago by
Ram
43k • written 2 days ago by
barrypraveen
▴ 130
1
vote
2
replies
222
views
Deseq generating warning "the model matrix is not full rank"
deseq
updated 1 day ago by
bioruffo
▴ 40 • written 2 days ago by
MAPK2
▴ 40
0
votes
0
replies
82
views
Metacoder plot_cladogram long calculation times
Metacoder
updated 2 days ago by
Ram
43k • written 2 days ago by
La52dA97b6
• 0
0
votes
2
replies
197
views
how to run limma for large datasets
R
HPC
biostatistics
statistics
updated 2 days ago by
Ram
43k • written 2 days ago by
Bioinfonext
▴ 460
1
vote
0
replies
96
views
Downloading immne signature and pathway signature genes form publication and KEGG
genes
TRANSCRIPTOME_signature
2 days ago by
mrazib0210
▴ 10
0
votes
1
reply
144
views
NCBI gene data
Variants
NCBI
updated 2 days ago by
GenoMax
140k • written 2 days ago by
chandrakala.m
• 0
0
votes
1
reply
139
views
How to perform GO enrichment analysis for assembled sequence ?
GO-enrichment
Gene-Ontology
updated 2 days ago by
Ram
43k • written 2 days ago by
Sony
▴ 10
1
vote
0
replies
108
views
checkm lineage.ms output file
checkm
lineage
3 days ago by
A_heath
▴ 160
0
votes
0
replies
211
views
diffbind : killed dba.count(DBsample, bParallel=FALSE)
diffbind
r
atacseq
3 days ago by
Pierre Lindenbaum
160k
0
votes
0
replies
95
views
OSCC Dataset downlod using TCGA biolink
R
OSSC
TCGAbiolink
GDC
updated 2 days ago by
Ram
43k • written 3 days ago by
Biogeek
• 0
2
votes
3
replies
213
views
Reference mouse phased vcf
mm10
vcf
phasing
Beagle
3 days ago by
machoo
• 0
0
votes
0
replies
83
views
Public datasets for genome-wide level mRNA-protein correlation calculation?
mRNA
protein
correlation
3 days ago by
Shicheng Guo
★ 9.4k
0
votes
0
replies
99
views
What is the usual basecalls length and reference mapping length relationship?
genome
alignment
rna-seq
updated 3 days ago by
Carlo Yague
8.6k • written 3 days ago by
anne
• 0
0
votes
1
reply
155
views
Difference in relative abundance between MicrobiomeDB and r phyloseq
phyloseq
updated 3 days ago by
Chris Dean
▴ 390 • written 3 days ago by
benkosta
• 0
0
votes
0
replies
140
views
beta coefficient improves after doing mediation analysis
coefficient
mediation
beta
regression
4 days ago by
rheab1230
▴ 140
0
votes
0
replies
146
views
Cromwell slurm singularity call caching
cromwell
singularity
wdl
4 days ago by
asmariyaz23
▴ 10
0
votes
1
reply
200
views
Getting error in alignment using STAR
STAR
Error
updated 5 days ago by
Michael
54k • written 5 days ago by
pavithra.bioinformatics
• 0
0
votes
1
reply
225
views
PCA script correction
correction
script
PCA
updated 5 days ago by
BioinfGuru
★ 1.6k • written 5 days ago by
prity6459
• 0
1
vote
13
replies
963
views
error when running phg create-maf-vcf to build a built practical haplotype graph (v2)
pangenome
phg_v2
plants
PHG
updated 2 days ago by
lcj34
▴ 410 • written 8 days ago by
b.contreras.moreira
▴ 70
0
votes
2
replies
286
views
PopGenome lost individual information
PopGenome
1 day ago by
Yixuan
• 0
2
votes
6
replies
452
views
Need help understanding core SNPs
SNPs
snippy
3 days ago by
ujichu
• 0
0
votes
0
replies
177
views
Only positive enrichment score in GSEA
enrichmentanalysis
clusterprofiler
gsea
bioconductor
rnaseq
5 days ago by
enee
▴ 10
0
votes
8
replies
405
views
Nextflow ERROR : Timeout waiting for connection from pool
nextflow
1 hour ago by
dzisis1986
▴ 70
0
votes
0
replies
163
views
working with shapeit.
shapeit
6 days ago by
sanchit000singhdr098
• 0
0
votes
0
replies
155
views
Motif Scanning: HOMER vs MEME, settings?
homer
fimo
6 days ago by
mb
• 0
0
votes
0
replies
164
views
How to identify the phylogenetic node age of RNAs?
phylogeny
genome
evolution
RNA-seq
6 days ago by
Apex92
▴ 280
0
votes
3
replies
297
views
How to proceed with downstream analysis after tumor-only snp calling using Varscan2?
snv
compressing
varscan
bcftools
5 days ago by
kabir.deb
▴ 80
0
votes
0
replies
177
views
Questions on demultiplexing using Qiime2
demultiplexing
barcode
6 days ago by
Minh
• 0
0
votes
0
replies
183
views
Problem encountered during Pearson Correlation Analysis between two immune cell subtypes
scRNA-seq
biostatistics
6 days ago by
applepie
• 0
0
votes
6
replies
406
views
Download Panther entry list
PANTHER
6 days ago by
Nicolas
• 0
0
votes
0
replies
177
views
Troubleshooting SCTransform Error in Seurat: "Can't use NA as row index in a tibble for assignment"
SCTransform
updated 6 days ago by
Ram
43k • written 6 days ago by
Anisha
• 0
0
votes
0
replies
170
views
scRNA Cell Clustering Defined by Normalized Counts
Normalization
scRNA
Seurat
6 days ago by
sakura
• 0
0
votes
0
replies
173
views
Example - Meta Analysis TCGA and DepMap
Meta-Analysis
TCGA
DepMap
updated 6 days ago by
Ram
43k • written 6 days ago by
joseph.landry
▴ 50
0
votes
1
reply
198
views
Extract Umi sequence to readname
Sequence
FgBio
UMI
updated 6 days ago by
GenoMax
140k • written 6 days ago by
Smilesky
• 0
1
vote
6
replies
461
views
Quest about the input data for PCA analysis
PCA
5 days ago by
tujuchuanli
▴ 100
2
votes
1
reply
207
views
Disease Prevalence Database/Disease Incidence Database
prevalence
updated 6 days ago by
Ram
43k • written 7 days ago by
Shicheng Guo
★ 9.4k
0
votes
0
replies
135
views
Tool for power calculation in GWAS for quantative trait
trait
quantative
power
calculation
GWAS
7 days ago by
chevivien
▴ 90
1
vote
1
reply
278
views
Advice for genetic diversity stats analysis with both variant and variant sites
pi
diversity
vcf
genetics
updated 7 days ago by
dthorbur
★ 1.7k • written 7 days ago by
ekirsch
• 0
1
vote
3
replies
251
views
How to validate the assembly completeness of unaligned reads ?
MaSuRCA
SPAdes
updated 7 days ago by
GenoMax
140k • written 7 days ago by
Sony
▴ 10
0
votes
1
reply
185
views
PEAR seems to have sense to me
PEAR
updated 7 days ago by
GenoMax
140k • written 7 days ago by
ManuelDB
▴ 80
0
votes
1
reply
168
views
Interprete plot of dispersion estimation by DESeq2
dispersion
DEXseq
DESeq2
updated 7 days ago by
Pierre Lindenbaum
160k • written 7 days ago by
tien
▴ 10
0
votes
1
reply
157
views
Adding gene to GRange objects with single base
GRanges
genomics
updated 7 days ago by
ATpoint
81k • written 7 days ago by
QX
• 0
0
votes
0
replies
148
views
Change orig.ident column in seurat meta.data to match cell barcode sample prefixes
seurat
8 days ago by
bgbs
• 0
351 results • Page
2 of 8
Recent Votes
Structural variant filtering
Trouble with bedtools getfasta
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
Answer: Hybrid assembly Pacbio- Nanopore
C: Why is 0/0 homozygous reference call in VCF useful information?
Answer: snippy error
Answer: TSS of protein coding genes
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Devon Ryan
104k
Popular Question
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blur
▴ 280
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ATpoint
81k
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Recent Replies
Comment: convert cds to seurat object
by
edoardofilippi1998
• 0
Did you check the data in the assay of the cell_data_set object?
Comment: calculate mismatch rate from VCF file
by
Pierre Lindenbaum
160k
use the output of `samtools mpileup`
Comment: Volcano Plot Output Inquiry: Graphs Facing Down
by
ATpoint
81k
It's `-log10(pvalue)`, you miss the minus. Some people use indeed pvalue, but since you're filtering on padj, I would show `-log10(padj)` r…
Comment: calculate mismatch rate from VCF file
by
Dora
▴ 10
Thank you for your reply!! My bad. I didn't mention that I want to get the mismatch rate for each site. Is this error rate for each site?
Comment: Interproscan taking so much time
by
dthorbur
★ 1.7k
Parallelize. Chunk your transcriptome into groups of something like 5000 (or less if you want it to go faster), and run an array across you…
Comment: Nanopore data filtering using fastp
by
dthorbur
★ 1.7k
Ah, sorry, I was thinking of the wrong command. You can either use `seqtk sample` or `seqkit sample`. I would recommend the former if your …
Comment: Variant calling of GBS data
by
analyst
▴ 10
It does not output warning when I skip flags for MQRankSum and ReadPosRankSum **java -jar -Xmx30G gatk.jar VariantFiltration -R reference…
Comment: Merging featureCounts output for different species
by
andrebolerbarros
• 0
Is there any list of homology you could use for this merging? Maybe this would be helpful
Comment: Variant calling of GBS data
by
Pierre Lindenbaum
160k
again, remove the spaces " "SOR > 10." -> " "SOR>10"
Comment: Variant calling of GBS data
by
analyst
▴ 10
It is still giving same warning java -jar -Xmx30G gatk.jar VariantFiltration -R reference.fa -V A_raw_snps.vcf -O A_filtered_snps.vcf --fi…
Comment: Nextflow ERROR : Timeout waiting for connection from pool
by
dzisis1986
▴ 70
It doesn't make sense how to change the threads and in my case it is not working! What kind of problem is that ? is it related to Amazon to…
Comment: STAR aligner options
by
theophile
• 0
I have finally found out the reason behind this behavior. As [pointed out by dsull][1], the beginning of the alignment of read1 to the rat…
Comment: Variant calling of GBS data
by
analyst
▴ 10
Right Pierre, thanks.
Comment: Variant calling of GBS data
by
Pierre Lindenbaum
160k
remove spaces in expressions. 'MQRankSum<0.4'
Comment: Variant calling of GBS data
by
analyst
▴ 10
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