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395 results • Page
5 of 8
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
123
views
Merging replicates from Encode project
CHIP-seq
encode
20 days ago by
Nurken
• 0
1
vote
3
replies
290
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
20 days ago by
WouterDeCoster
47k
1
vote
3
replies
326
views
some error in building kraken2 database
metagenome
kraken2
19 days ago by
Art1ess
• 0
0
votes
1
reply
204
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 20 days ago by
bk11
★ 2.4k • written 20 days ago by
Susmita Mandal
▴ 110
1
vote
1
reply
206
views
Failed kmer content
kmer
illumina
ngs
updated 20 days ago by
Ram
43k • written 20 days ago by
Kasturi
• 0
0
votes
0
replies
111
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 20 days ago by
Ram
43k • written 20 days ago by
SSSJec
• 0
0
votes
1
reply
172
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 21 days ago by
Ram
43k • written 21 days ago by
Cameron.walker9900
• 0
0
votes
8
replies
437
views
Error in cnetplot enrichplot package
R
updated 21 days ago by
Ram
43k • written 21 days ago by
Farhad
• 0
0
votes
0
replies
126
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 21 days ago by
Ram
43k • written 21 days ago by
maxime.policarpo
▴ 200
0
votes
0
replies
112
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 21 days ago by
Ram
43k • written 21 days ago by
sansan_96
▴ 90
0
votes
0
replies
115
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 20 days ago by
Ram
43k • written 21 days ago by
Amélie
• 0
0
votes
0
replies
220
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 21 days ago by
Ram
43k • written 21 days ago by
Pine
▴ 20
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink
PED
updated 21 days ago by
chrchang523
10k • written 6.2 years ago by
Ginevra
▴ 10
1
vote
8
replies
519
views
Downsampling fastq file
downsample
fastq
13 days ago by
marco.barr
▴ 100
0
votes
1
reply
164
views
tbtool
tbtool
updated 21 days ago by
Ram
43k • written 21 days ago by
Raman
• 0
0
votes
10
replies
588
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 13 days ago by
i.sudbery
19k • written 21 days ago by
Patadu94
• 0
0
votes
1
reply
155
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 21 days ago by
ATpoint
82k • written 21 days ago by
enanoide
• 0
0
votes
0
replies
103
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
21 days ago by
manaswwm
▴ 510
0
votes
0
replies
94
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
20 days ago by
alifafiq1
• 0
0
votes
0
replies
100
views
How to get somatic variation based on RNA-seq data?
RNA-seq
variation
somatic
21 days ago by
feather-W
• 0
2
votes
4
replies
365
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
19 days ago by
samuelkalandarov2002
▴ 10
0
votes
0
replies
97
views
Annotating single cell data automatically
cell
annotation
single
21 days ago by
Gerard
• 0
0
votes
1
reply
191
views
RNA-seq bacteria contamination
RNA-seq
updated 21 days ago by
GenoMax
142k • written 21 days ago by
sh
• 0
0
votes
0
replies
92
views
Imputation advice
imputation
21 days ago by
kl
▴ 10
0
votes
0
replies
114
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
21 days ago by
Enrique
• 0
0
votes
0
replies
90
views
Correct way of reducing predictive model complexity
lasso
glmnet
predictvemodeling
regression
21 days ago by
sativus
▴ 20
0
votes
0
replies
95
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER
MARINA
ARACNe
21 days ago by
Biostars2200
• 0
0
votes
0
replies
155
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 21 days ago by
Carlo Yague
8.7k • written 21 days ago by
Atul K.
• 0
2
votes
5
replies
524
views
Marking duplicates using UMIs
Deduplication
UMI
updated 21 days ago by
i.sudbery
19k • written 23 days ago by
Lipika
• 0
0
votes
0
replies
156
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 22 days ago by
Ram
43k • written 23 days ago by
sainavyav22
• 0
0
votes
0
replies
160
views
Bacterial genome alignment with mauve
Bacteria
mauve
genome
23 days ago by
rthapa
▴ 90
0
votes
0
replies
155
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation
CGenFF
Gromacs
VMD
23 days ago by
Mamatha Y S
• 0
0
votes
2
replies
314
views
bam merging for archaic samples
samtools
bam
updated 22 days ago by
Ram
43k • written 23 days ago by
Matteo Ungaro
▴ 100
1
vote
0
replies
560
views
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers
TRINITY
23 days ago by
mathavanbioinfo
▴ 90
2
votes
5
replies
772
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 23 days ago by
Jesse
▴ 770 • written 24 days ago by
Ann
★ 2.4k
0
votes
0
replies
204
views
agilent microarray gpl data does not have gene symbol column
microarray
agilent
gpl
updated 24 days ago by
Ram
43k • written 24 days ago by
mja
• 0
0
votes
0
replies
206
views
scRNA Cluster frequency
CV
PCA
scRNA
Cluster-Frequency
24 days ago by
Nitin
• 0
0
votes
0
replies
198
views
Chemical structure validation
structure
cap
validation
metabolite
24 days ago by
Rodolfo Adrián
• 0
0
votes
1
reply
296
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 24 days ago by
GenoMax
142k • written 24 days ago by
bioyas
▴ 10
0
votes
0
replies
230
views
Copy number variation plot
Copy-number-variation
genomics
updated 24 days ago by
Ram
43k • written 24 days ago by
Emmi
• 0
0
votes
0
replies
205
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs
ngsTools
ANGSD
genomics
24 days ago by
DanielEB_fisk
▴ 20
0
votes
1
reply
317
views
Could you please assist in identifying this cluster?
single-cell
updated 24 days ago by
Ram
43k • written 24 days ago by
carolofharvest
▴ 40
0
votes
0
replies
222
views
Conversion to tree format
PLINK
bed
Figtree
SplitsTree
updated 24 days ago by
Ram
43k • written 24 days ago by
Dinmukhamed
• 0
0
votes
0
replies
214
views
miRDeep2: How to get the read counts
mirdeep2
24 days ago by
Atul K.
• 0
0
votes
0
replies
219
views
Lncipedia GTF file error
Proteomics
updated 24 days ago by
Ram
43k • written 24 days ago by
atharvakarkare14
▴ 30
3
votes
3
replies
544
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 23 days ago by
swbarnes2
14k • written 24 days ago by
noodle
▴ 580
0
votes
2
replies
586
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
25 days ago by
航太郎
• 0
0
votes
0
replies
232
views
create genewise sync file in popoolation
popoolation
updated 25 days ago by
GenoMax
142k • written 25 days ago by
N.Y.Wiyana-Hewage
• 0
0
votes
2
replies
419
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
24 days ago by
Ashok
• 0
0
votes
2
replies
461
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
24 days ago by
Ashok
• 0
395 results • Page
5 of 8
Recent Votes
Comment: How does gene length effect the number of reads mapped
Comment: How does gene length effect the number of reads mapped
Comment: How does gene length effect the number of reads mapped
Comment: How does gene length effect the number of reads mapped
A: Filtering of VCF, INFO DP or FORMAT DP
What is the difference between GRCh37 and hs37? And hg19?
Answer: Duplicated sequence samtools
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Recent Replies
Comment: Help with IGV abbreviation
by
GeneC
• 0
Thank you for the link and details
Comment: Help with IGV abbreviation
by
GeneC
• 0
Thank you very much for helping with the details.
Comment: How does gene length effect the number of reads mapped
by
Chen
• 0
thank you :)
Answer: Filtering based on alternate allelic balance
by
Arton
• 0
I found the answer when using bcftools. Is there is a way to do this with FilterVcf? bcftools filter --include '(FMT/AD[0:1])/(FMT/A…
Comment: Help with IGV abbreviation
by
GenoMax
142k
Those are SAM format fields. Check section 1.4 here: https://samtools.github.io/hts-specs/SAMv1.pdf > 1:2114:12111:13792 That is part of …
Answer: Help with IGV abbreviation
by
Mathew
▴ 120
Hi, here is a breakdown of each part that you asked about: **flag 99**: This indicates various properties of the read alignment. In this c…
Comment: Kraken2 database
by
Mathew
▴ 120
I don't see any databases with just pathogenic bacteria genomes from just a quick search, I would imagine that using the Standard-16 databa…
Comment: Galaxy StringTie error
by
Mathew
▴ 120
I am not sure if this is true for Galaxy, but when I code in Python, SyntaxWarning: invalid escape sequence '' occurs when you want to add …
Comment: Can diamond prepdb be used to make a taxonomically aware database?
by
GenoMax
142k
Should be possible: https://www.biostars.org/p/430366/ Are you using an older version of `diamond`? Latest versions of `diamond` can use N…
Comment: SNPEff database building error
by
Fungal genetics
• 0
Hi, Below SNPEff database building error I am getting. "FATAL ERROR: Most Exons do not have sequences!" The headers are correct and sam…
Comment: Extracting named fasta sequences according to list with Biopython
by
Rubayetul
• 0
the last line of SeqIO.write(record.....'fasta') in a for loop will input the the last record into new fasta file and it will only contain …
Comment: How to process Bulk WES data?
by
GenoMax
142k
You could use `sarek` (nf-core's exome pipeline) if you don't want to customize or reinvent : https://nf-co.re/sarek/3.4.2
Comment: Empty .best and .sing2 Files After Running Demuxlet
by
Ram
43k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Answer: FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last plac
by
David Langenberger
11k
Two last seats have just become available. Apply now, if you want them.
Comment: featureCounts output summary assigned value higher than uniquely mapped reads fr
by
GenoMax
142k
You always need to add the following option when you are using `-p` to count paired-end reads. --countReadPairs If specified, fragm…
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