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1,000 results • Page
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0
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1.7k
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How to handle NaN in emmax Kinship matrix?
GWAS
SNP
updated 3 days ago by
Thu
• 0 • written 5.1 years ago by
CWesse
• 0
1
vote
3
replies
182
views
Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
RNA-evidence
genome
prediction
masking
updated 3 days ago by
Darked89
4.4k • written 3 days ago by
Ayish
• 0
0
votes
1
reply
121
views
What is the possibility of Depth (DP) being higher than the coverage
GATK
DP
Coverage
Depth
HaplotypeCaller
updated 3 days ago by
seidel
11k • written 3 days ago by
dare_devil
★ 3.1k
0
votes
2
replies
192
views
What does "OS_CNSR" and "PFS_CNSR" mean?
survival
cancer
r
3 days ago by
JACKY
▴ 100
0
votes
1
reply
132
views
CIBERSORT Error: File not found
CIBERSORT
updated 3 days ago by
ATpoint
73k • written 3 days ago by
jcara514
• 0
3
votes
4
replies
267
views
retaining only the clusters of interest
seurat
single-cell
scRna-seq
updated 3 days ago by
Ram
39k • written 3 days ago by
shamza
• 0
0
votes
3
replies
276
views
Gviz Coverage Plots
gviz
scrnaseq
cellranger
r
updated 3 days ago by
Ram
39k • written 3 days ago by
Researcher
• 0
1
vote
0
replies
131
views
Alternative approach to rarefying in 16S rRNA analysis
16S
Rarefying
rRNA
4 days ago by
zhangdengwei
▴ 190
1
vote
2
replies
227
views
phage genome submission in ncbi genebank
phage
table2asn
ncbi
3 days ago by
tahsinkhan570
• 0
2
votes
3
replies
274
views
Same GEO Accession, different SRR number, how to download this RNA-seq paired-end data?
sra-toolkit
fastq
RNA-seq
SRA
updated 4 days ago by
GenoMax
130k • written 4 days ago by
ev97
• 0
0
votes
0
replies
129
views
Which is the minor allele in ped file in plink?
plink
updated 4 days ago by
GenoMax
130k • written 4 days ago by
khn
▴ 130
0
votes
2
replies
234
views
Correct way to remove Nextera adapters from ITS sequences
adapters
ITS
trimmomatic
3 days ago by
mattze731
▴ 10
0
votes
0
replies
123
views
What statistical test should I use to analyse my two set of transcriptomique data?
transcriptome
4 days ago by
F.Bedjou
▴ 10
0
votes
0
replies
102
views
Difference MITOS WebServer and MITOS 2 Webserver
MITOS2
WebServer
Difference
MITOS
4 days ago by
hashim.rana11
▴ 20
0
votes
0
replies
124
views
Integrate RDS files
integration
4 days ago by
Andy
▴ 50
0
votes
1
reply
181
views
Information on sequin RNA spike in standards
Sequin
Spike-in
RNA-seq
updated 3 days ago by
ATpoint
73k • written 4 days ago by
akainth
▴ 10
1
vote
9
replies
377
views
Trying to edit VCF file
VCF
R
bcftools
snpsaurus
updated 4 days ago by
Ram
39k • written 4 days ago by
peavy
• 0
0
votes
1
reply
389
views
How to quantification proteomics data
proteomics
updated 4 days ago by
eqoa45
• 0 • written 19 months ago by
LeeLee
▴ 10
1
vote
4
replies
250
views
Is hg38 on the multiz 30-way alignment inaccurate?
maf
UCSC
PHAST
multiz
4 days ago by
Daniel
▴ 30
0
votes
2
replies
1.5k
views
How to perform statistical analysis of label free experiment using results from Proteome Discoverer?
Proteome-Discoverer
Label-Free
Proteomics
updated 4 days ago by
Ram
39k • written 4.5 years ago by
k2bhide
▴ 80
0
votes
0
replies
115
views
Label free quantification in Proteome discoverer software
proteomics
quantification
spectrometry
shotgun
4 days ago by
eqoa45
• 0
1
vote
0
replies
118
views
How to predict gene amplification from RNAseq and ATACseq data?
amplification
ATAC
5 days ago by
Dan
▴ 120
1
vote
2
replies
198
views
hisat2 Error 137
hisat2
RNA-seq
4 days ago by
Forough
▴ 10
0
votes
1
reply
180
views
Error occured at the PHG imputation step: allele in genotype not in the variant context
PHG
Imputation
PracticalHaplotypeGraph
Haplotype
updated 2 days ago by
lcj34
▴ 230 • written 5 days ago by
xeod21
• 0
3
votes
6
replies
381
views
Embryo transcriptome
database
transcriptome
SRA
updated 3 days ago by
Basti
★ 1.6k • written 5 days ago by
firefox91
• 0
1
vote
3
replies
213
views
Obtain a --gene-trans-map file after rnaSPAdes
rnaSPAdes
Trinity
5 days ago by
UserA
• 0
0
votes
0
replies
97
views
How to extract only neutral markers from low-coverage whole genome sequencing?
low-coverage
whole-genome-sequencing
updated 5 days ago by
Ram
39k • written 5 days ago by
beausoleilmo
▴ 530
0
votes
4
replies
240
views
Difference between USCS exon coordinates and ensembl
exons
Ensembl
5 days ago by
amy__
▴ 50
0
votes
0
replies
95
views
Why sone miRNAs are not present in TCGA data
TCGA
miRNA
RNA-seq
5 days ago by
nicolo.gualandi
• 0
0
votes
0
replies
89
views
Prediction of altrered metabolites from altered gene expression
Gene
Metabolites
5 days ago by
english.server
▴ 290
0
votes
6
replies
387
views
variant allelic fraction
vep
updated 4 days ago by
Ram
39k • written 5 days ago by
Jom
• 0
0
votes
1
reply
160
views
Pairwise Alignment
Pairwise-Alignment
updated 5 days ago by
Ram
39k • written 5 days ago by
Fatemeh
• 0
0
votes
0
replies
99
views
How to perform a phylogenetic analysis from a vcf file
variants
haplotyping
phylogeny
vcf
6 days ago by
rj.rezwan
• 0
0
votes
2
replies
215
views
Where to get the molecular subtype information of STAD sample in TCGA
TCGA
database
9 hours ago by
younglin113
▴ 50
0
votes
0
replies
143
views
How to keep ComplexHeatmap from reordering annotations
Dendrogram
HeatmapAnnotations
R
Heatmap
ComplexHeatmap
6 days ago by
Manuel
• 0
2
votes
3
replies
261
views
Differential protein expression analysis
R
proteomic
statistics
updated 3 days ago by
dsull
★ 4.2k • written 6 days ago by
Ribo
▴ 40
0
votes
3
replies
338
views
(ERR): "index/Trinity.fa" does not exist or is not a Bowtie 2 index Exiting now ...
bowtie2
align_stats
trinity
5 days ago by
eimanpharmacist
▴ 20
0
votes
4
replies
390
views
What are recommended parameters for the local protein alignment ?
protein
alignment
6 days ago by
Alexander
▴ 110
0
votes
0
replies
134
views
microsatellite, SSR, using Galaxy
Galaxy
SSR
using
microsatellite
7 days ago by
m.esmaeilpour
▴ 10
0
votes
0
replies
155
views
decoupleR & Transcription Factory Activity Inference: pvalue or padj?
pvalue
padj
decoupleR
7 days ago by
OST
▴ 10
2
votes
3
replies
352
views
Low mapping percentage
mapping
STAR
RNAseq
6 days ago by
Sib
▴ 40
0
votes
0
replies
178
views
Visualization App for RNASeq Differential Expression and Enrichment Analysis
differential
visualization
RNASeq
analysis
expression
enrichment
7 days ago by
Mark
• 0
0
votes
0
replies
164
views
busco id description
OrthoDB
BUSCO
updated 7 days ago by
Ram
39k • written 8 days ago by
angelina
• 0
0
votes
5
replies
408
views
how to Construct a Newick tree file from five large fasta files
tree
Newick
alignment
updated 7 days ago by
Joe
21k • written 8 days ago by
gunala.nikhil
• 0
0
votes
0
replies
165
views
NMDS plotting issue
NMDS
metagenomic
8 days ago by
arshad1292
▴ 90
0
votes
2
replies
254
views
featurecounts not working on mirbase annotation file
usegalaxy
miRNA-seq
4 days ago by
demoraesdiogo2017
▴ 90
0
votes
0
replies
143
views
IGV insertions
insertions
IGV
8 days ago by
christoph.schubart
• 0
1
vote
0
replies
163
views
Bayesian network for biological data using bnlearn
bnlearn
RNA-seq
bayesian-network
updated 7 days ago by
Ram
39k • written 8 days ago by
priyankamehta.1811
▴ 10
0
votes
0
replies
150
views
jellyfish options
kmer
jellyfish
8 days ago by
Tele
• 0
1
vote
3
replies
238
views
hardfilter error
bam
recall
8 days ago by
bestone
▴ 20
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Answer: featureCounts Output "The reads are assigned on the single-end mode"
Answer: HTSeq count stranded setting
Answer: Salmon Index
Answer: Solving environment: failed with initial frozen solve. Retrying with flexible so
Answer: Solving environment: failed with initial frozen solve. Retrying with flexible so
Comment: Solving environment: failed with initial frozen solve. Retrying with flexible so
Comment: GISTIC from ASCAT
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Recent Replies
Comment: multiqc: group samples by population + boxplot ?
by
Pierre Lindenbaum
155k
It worked by parsing a first run of multiqc, extract the data from the sanitised data , create a SVG plot with R, include the SVG into a fi…
Comment: Solving environment: failed with initial frozen solve. Retrying with flexible so
by
Ahmed
▴ 10
thanks, bro I get the solve of my problem by installing new environment and reinstalling samtools software again.
Comment: Solving environment: failed with initial frozen solve. Retrying with flexible so
by
Ahmed
▴ 10
Thanks for telling me that, and i apologize for bad explanation because I am beginner user with the site!
Comment: amrfinder not working on loop?
by
Pierre Lindenbaum
155k
what is the output of the following commands: ls -lah '/home/bvs/neelam/AMRFINDER_hypo/hypothetical_analysis/P_aeruginosa_RP73.fasta' …
Comment: amrfinder not working on loop?
by
GenoMax
130k
> Cannot open file > '/home/bvs/neelam/AMRFINDER_hypo/hypothetical_analysis/P_aeruginosa_RP73.fasta' Looks like either the file path is in…
Comment: R ggplot
by
Ram
39k
Is "R ggplot" the most concise/descriptive title you can use?
Answer: Solving environment: failed with initial frozen solve. Retrying with flexible so
by
Ram
39k
1. `bioconda` is a conda channel, not a command. I'm surprised it executes some sort of binary - what is the output of `alias bioconda` and…
Comment: Solving environment: failed with initial frozen solve. Retrying with flexible so
by
Ram
39k
Use proper tags - in your previous post, you pasted the question text in the tag field and here, your tag is `nothing`. Use relevant tags (…
Comment: hisat2-align exited with value 1
by
Ahmed
▴ 10
thanks man <3 you saved me!!
Comment: no output from GATK CombineGVCFs
by
Pierre Lindenbaum
155k
> The number of gVCFs in the list has a hard limit no, I don't think so. But if you have 10000 VCFs, you should combine 100x100 VCFS and …
Comment: novel miRNA naming(annotation)
by
kuttibiotech2009
▴ 30
Do you have any idea about it?. I also want to do the same.
Answer: Identify similarly mapped reads in BAM/SAM?
by
Pierre Lindenbaum
155k
bedtools bamtobed -i in.bam | datamash -g 1,2,3 collapse 4
Comment: GISTIC from ASCAT
by
Hyper_Odin
▴ 290
Also, I would like to add that we cannot use ASCAT output for GISTIC input...since GISTIC expects all the chromosomes in the input file eve…
Comment: GISTIC from ASCAT
by
Hyper_Odin
▴ 290
Hi, Ram thanks for the help...I figured out the issue. somehow I had duplicate files in the folder which caused the issue.
Answer: multiqc: group samples by population + boxplot ?
by
Phil Ewels
★ 1.2k
You can't group and make boxplots as you describe, probably your best bet is to use the [highlight tool][1] in the report (especially if yo…
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