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128 results • Page
2 of 3
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Views
Votes
Replies
0
votes
2
replies
306
views
GSEA analysis in R
GSEA
R
Arabidopsis
6 days ago by
Sudip
• 0
0
votes
1
reply
277
views
Could you please assist in identifying this cluster?
single-cell
updated 5 days ago by
Ram
43k • written 5 days ago by
Kazo
• 0
0
votes
0
replies
272
views
Choice of relatedness cutoff for GWAS of a large cohort (>100K samples)
relatedness
IBD
GWAS
updated 1 day ago by
Ram
43k • written 14 months ago by
Oak
▴ 10
0
votes
8
replies
267
views
Error in cnetplot enrichplot package
R
updated 1 day ago by
Ram
43k • written 1 day ago by
Farhad
• 0
1
vote
2
replies
267
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 6 days ago by
Ram
43k • written 7 days ago by
aniigodwinn
• 0
0
votes
1
reply
261
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 6 days ago by
GenoMax
141k • written 6 days ago by
ycts
• 0
0
votes
1
reply
257
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 4 days ago by
GenoMax
141k • written 5 days ago by
bioyas
▴ 10
0
votes
2
replies
248
views
bam merging for archaic samples
samtools
bam
updated 3 days ago by
Ram
43k • written 4 days ago by
Matteo Ungaro
▴ 100
0
votes
5
replies
246
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
5 hours ago by
njornet
▴ 20
1
vote
5
replies
234
views
Downsampling fastq file
downsample
fastq
updated 2 days ago by
Ram
43k • written 2 days ago by
marco.barr
▴ 80
2
votes
4
replies
228
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
8 hours ago by
samuelkalandarov2002
▴ 10
1
vote
2
replies
225
views
permutation test in edgeR
rna-seq
edgeR
updated 2 days ago by
Gordon Smyth
★ 7.0k • written 16 days ago by
Netanel
• 0
1
vote
1
reply
221
views
Retrieve a % coverage for each transcript
RNA-seq
updated 6 days ago by
Ram
43k • written 6 days ago by
jammydodger123456
▴ 40
1
vote
3
replies
220
views
some error in building kraken2 database
metagenome
kraken2
14 hours ago by
Art1ess
• 0
0
votes
0
replies
208
views
create genewise sync file in popoolation
popoolation
updated 5 days ago by
GenoMax
141k • written 5 days ago by
N.Y.Wiyana-Hewage
• 0
0
votes
0
replies
207
views
Variant Generation Using Longshot
long-reads
variant-calling
ONT
minion
longshot
updated 6 days ago by
Ram
43k • written 6 days ago by
samuelkalandarov2002
▴ 10
0
votes
0
replies
205
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
3 days ago by
abhishekghadge
• 0
0
votes
0
replies
201
views
Copy number variation plot
Copy-number-variation
genomics
updated 5 days ago by
Ram
43k • written 5 days ago by
Emmi
• 0
0
votes
0
replies
198
views
Lncipedia GTF file error
Proteomics
updated 5 days ago by
Ram
43k • written 5 days ago by
atharvakarkare14
▴ 10
0
votes
0
replies
197
views
traying to make a maf from an already annotated vcf
vcf
vcf2maf
maf
maftools
VEP
2 days ago by
Javier
• 0
0
votes
0
replies
192
views
Conversion to tree format
PLINK
bed
Figtree
SplitsTree
updated 5 days ago by
Ram
43k • written 5 days ago by
Dinmukhamed
• 0
0
votes
0
replies
190
views
miRDeep2: How to get the read counts
mirdeep2
5 days ago by
Atul K.
• 0
0
votes
0
replies
185
views
absolute path for symbolic links in Snakefile
Snakemake
updated 4 days ago by
Ram
43k • written 4 days ago by
yifangt86
▴ 60
0
votes
0
replies
185
views
scRNA Cluster frequency
CV
PCA
scRNA
Cluster-Frequency
4 days ago by
Nitin
• 0
1
vote
3
replies
184
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
1 day ago by
WouterDeCoster
47k
0
votes
0
replies
182
views
agilent microarray gpl data does not have gene symbol column
microarray
agilent
gpl
updated 4 days ago by
Ram
43k • written 4 days ago by
mja
• 0
0
votes
1
reply
181
views
Heatmap and rna-seq
RNA-Seq
Heatmap
and
updated 18 hours ago by
Istvan Albert
100k • written 1 day ago by
qudrat.nii
▴ 10
0
votes
0
replies
178
views
Chemical structure validation
structure
cap
validation
metabolite
4 days ago by
Rodolfo Adrián
• 0
0
votes
2
replies
175
views
How to calculate identity percentage between proteins contained in a FASTA file?
percentage
FASTA
alignment
identity
updated 8 hours ago by
b.contreras.moreira
▴ 170 • written 19 hours ago by
v.berriosfarias
▴ 140
0
votes
2
replies
173
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 1 day ago by
i.sudbery
19k • written 2 days ago by
Patadu94
• 0
0
votes
0
replies
174
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs
ngsTools
ANGSD
genomics
5 days ago by
DanielEB_fisk
▴ 20
0
votes
0
replies
172
views
Pruning with plink finds a majority of SNPs in very high LD
LD
SNP
plink
pruning
6 days ago by
enferdeflame
• 0
0
votes
0
replies
171
views
How to root an unrooted tree with a known root tree?
phylogenetics
rooting
R
6 days ago by
P.
• 0
0
votes
0
replies
169
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
6 days ago by
synat.keam
▴ 100
0
votes
0
replies
163
views
Issues with SnpEff Assuming Circular Chromosomes in Eukaryotic Genome Analysis
snpEff
6 days ago by
ekirsch
• 0
0
votes
0
replies
162
views
Struggling to lift genome builds
PLINK
liftover
GWAS
updated 6 days ago by
GenoMax
141k • written 7 days ago by
srimmer
• 0
0
votes
0
replies
155
views
How can I obtain the tissue or sample name alongside the Tau score in tspex?
tau-score
tspex
updated 6 days ago by
Ram
43k • written 6 days ago by
bioinfo223
▴ 10
1
vote
1
reply
147
views
Failed kmer content
kmer
illumina
ngs
updated 1 day ago by
Ram
43k • written 1 day ago by
Kasturi
• 0
0
votes
2
replies
140
views
clustalo - align milions of short seq, memory issue
memory
clustalo
updated 1 day ago by
Mensur Dlakic
★ 27k • written 2 days ago by
emmanouil.a
▴ 120
0
votes
1
reply
136
views
RNA-seq bacteria contamination
RNA-seq
updated 2 days ago by
GenoMax
141k • written 2 days ago by
sh
• 0
0
votes
0
replies
136
views
Bacterial genome alignment with mauve
Bacteria
mauve
genome
3 days ago by
rthapa
▴ 90
0
votes
0
replies
134
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 3 days ago by
Ram
43k • written 3 days ago by
sainavyav22
• 0
0
votes
0
replies
131
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 1 day ago by
Ram
43k • written 1 day ago by
Oak
▴ 10
0
votes
1
reply
130
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 1 day ago by
Ram
43k • written 1 day ago by
Cameron.walker9900
• 0
0
votes
0
replies
129
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation
CGenFF
Gromacs
VMD
3 days ago by
Mamatha Y S
• 0
0
votes
1
reply
125
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 1 day ago by
GenoMax
141k • written 1 day ago by
Srinka
▴ 20
0
votes
1
reply
118
views
tbtool
tbtool
updated 2 days ago by
Ram
43k • written 2 days ago by
Raman
• 0
0
votes
0
replies
116
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 2 days ago by
Carlo Yague
8.7k • written 2 days ago by
Atul K.
• 0
0
votes
1
reply
116
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 1 day ago by
bk11
★ 2.3k • written 1 day ago by
Susmita Mandal
▴ 110
0
votes
1
reply
112
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 2 days ago by
ATpoint
82k • written 2 days ago by
enanoide
• 0
128 results • Page
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Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.3k
This looks good. Please try with using `--allow-no-sex flag` plink --bfile your_data_phenoUP --assoc --allow-no-sex --out your_data_ph…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
SC899359_PC75420_A05 SC899359_PC75420_A05 0 0 0 2 SC899360_PC75415_D01 SC899360_PC75415_D01 0 0 0 2 SC899361_PC75425_H05 SC899361_PC75425_H…
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.3k
Please show me a few lines of phenotype updated .fam file. You can do `head your_data_phenoUP.fam` and paste result here. Please do not us…
Comment: GEMMA GWAS how to specify factor or numerical for covariates
by
Sofia
• 0
Hi, I don't have a solution to your question but I followed this tutorial and was helpful to me in my analysis https://youtu.be/NusV6duyvXs…
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas
by
GenoMax
141k
Catalog file lists the genomes included. There seem to be 71365 unique items in field 2. 2 Bacteria WP_000018326.1 4459…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
yes sure ! ![enter image description here][1] [1]: /media/images/f0f94f6c-4387-4188-a1aa-19152a89
Answer: AGeNT LocatIt
by
Greg
• 0
Give it more memory. ~10x more memory, or whatever you can give it, I had samples that weren't even close to being done after 3.5 da…
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas
by
Bertalan_Takacs
▴ 90
Thanks! I've already tried looking through these files, I need release 83. I am trying to find this information in the .catalog file of the…
Answer: Is it possible to get a list of representative genomes from a past RefSeq releas
by
GenoMax
141k
Possibly. You will need to know the RefSeq release version. Check in this directory: https://ftp.ncbi.nlm.nih.gov/refseq/release/release-ca…
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.3k
Hey, can you please show me a few lines of your phenotype updated .fam file? I m seeing there are 7 columns in it, that might be the proble…
Comment: PCA plot (Suggestions Needed)
by
jkim
▴ 170
How much variance were explained by PC1 and PC2? It doesn't look like that the largest source of variation came from the genotype differenc…
Comment: How to trim transcripts using information from NCBI contamination screen report
by
Lada
▴ 30
Thank you and yes, I agree going step back is the best option but I am in a hurry at the moment so I just need to stick to the transcriptom…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
Thank you so much for helping me out! I did the steps you mentioned but still got the same issue as shown in the snapshot ![enter image des…
Comment: different FeatureCounts output for the same data
by
Istvan Albert
100k
Make sure you are using the same version of featureCounts, it has changed how it deals with paired end reads. The exact same command will p…
Comment: Wilcox test using data slot (log normalized count values) of scRNA-seq between t
by
mropri
▴ 150
Thank you, will do Wilcox for now as I only have one control and one treatment, as I get more control and treatment samples, will stick wit…
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