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1,000 results • Page
1 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
5
replies
44
views
bcftools stats: definition of indel type
vcf
bcftools
1 hour ago by
WouterDeCoster
46k
0
votes
1
reply
33
views
BED file from GSEA gene set
ChIP-seq
BED
ChIP
bioinformatics
GSEA
file
updated 19 minutes ago by
ATpoint
61k • written 2 hours ago by
2138493o
▴ 20
0
votes
3
replies
77
views
Which data files are required to find GWAS summary statistics?
plink
updated 2 hours ago by
4galaxy77
★ 1.7k • written 3 hours ago by
Raju
• 0
0
votes
3
replies
107
views
How to install PEERTOOLS in a cluster?
linux
Peertools
GWAS
predictdb
unix
updated 3 hours ago by
solomoncharles77
▴ 90 • written 4 hours ago by
fernandogs97
• 0
0
votes
0
replies
24
views
WES -> recalibration matrix and Deduplication matrix reads number is very strange.
matrix
recal
dedup
reads
5 hours ago by
jk.kim
• 0
0
votes
0
replies
38
views
Palimpsest deconvolution_fit() problem
palimpsest
de
mutation
signature
extraction
novo
9 hours ago by
15927207765
• 0
1
vote
1
reply
122
views
convert csv to fasta format using python
python
updated 2 hours ago by
Joe
20k • written 11 hours ago by
Abdellrhmanakl
• 0
0
votes
0
replies
64
views
Read counts an order of magnitude higher on one chromosome
novaseq
alignment
Rad-seq
sequencing
demultiplex
11 hours ago by
Samuel
• 0
0
votes
5
replies
172
views
EGA (ENA) database wont accept fastq files
ENA
EGA
fastq
updated 2 hours ago by
lieven.sterck
13k • written 12 hours ago by
heskett
▴ 80
0
votes
4
replies
170
views
Split fastq files
Fastq
split
novaseq
updated 1 hour ago by
GenoMax
115k • written 13 hours ago by
zeina-younes
• 0
0
votes
0
replies
43
views
qPCR Assay plot
barplot
qpcr
R
14 hours ago by
Maria17
• 0
0
votes
2
replies
73
views
Error in GATK haplotypecaller running
GATK
updated 15 hours ago by
Ram
36k • written 15 hours ago by
Azhar Jameel
• 0
2
votes
7
replies
177
views
error while using cyvcf2 to parse the vcf file
error
vcf
cyvcf2
htslib
parsing
14 hours ago by
rheab1230
▴ 50
0
votes
0
replies
44
views
CNV and DUP in vcf files Gnomad database
dup
cnv
gnomad
vcf
17 hours ago by
arya.sagittarius
• 0
0
votes
1
reply
63
views
counting snps from alternative allele using tsv format
python
updated 17 hours ago by
Pierre Lindenbaum
145k • written 17 hours ago by
Abdellrhmanakl
• 0
0
votes
5
replies
121
views
blast with multithreads is much slower
blast
15 hours ago by
biobiu
▴ 130
0
votes
0
replies
72
views
What conclusions can I draw from a Procrustes Superimposition Test?
Multivariate
Statistics
Procrustes
Correlation
13 hours ago by
dch014
• 0
0
votes
7
replies
197
views
GSEA not returning significant gene sets
GSEA
updated 6 hours ago by
ATpoint
61k • written 18 hours ago by
jabbari.parnian
▴ 20
0
votes
1
reply
63
views
bcl2fastq error: Barcode lengths in the sample sheet do not match those in --use-bases-mask
cellranger
bcl2fastq
CITE
mkfastq
CITE-seq
updated 16 hours ago by
GenoMax
115k • written 18 hours ago by
coteparker
• 0
0
votes
3
replies
103
views
SRR sample ID
TCGAbiolinks
RNA-seq
sampleID
R
cancer
programming
updated 16 hours ago by
Hamid Ghaedi
★ 2.5k • written 19 hours ago by
mahsa
• 0
0
votes
0
replies
40
views
guppy_barcoder - demultiplex- custom barcodes
nanopore
guppy
demultiplex
updated 20 hours ago by
Ram
36k • written 20 hours ago by
henry-keen
▴ 20
1
vote
1
reply
77
views
DESeq2 and WGCNA
DESeq2
RNAseq
WGCNA
updated 5 hours ago by
Basti
▴ 340 • written 20 hours ago by
pthom010
▴ 20
0
votes
0
replies
41
views
Inferring GRN without transcription factor motif
scenic
GRN
cell
single
20 hours ago by
William
• 0
1
vote
3
replies
157
views
Can I compare different RNAseq experiment DEG lists to see which experiments are the most similar?
DEG
lists
Comparision
RNAseq
updated 20 hours ago by
rpolicastro
8.2k • written 22 hours ago by
rachel.walters.18
• 0
0
votes
5
replies
147
views
Method to fill N gaps with de novo assembly
assembly
updated 23 hours ago by
samuel.a.odonnell
▴ 330 • written 1 day ago by
pablo
▴ 210
0
votes
2
replies
136
views
How can I convert this format of S. tuberosum gene sequence ID - Soltu.DM.10G013850.1 - to Entrez ID?
potatoID
4 hours ago by
Sanja
• 0
0
votes
2
replies
105
views
panX no working
panX
error
9 hours ago by
saifulislam99121
• 0
0
votes
2
replies
115
views
SNP and Phenotype Correlation
Phenotype
Statistical
SNP
Correlation
R
8 hours ago by
chimerajit
• 0
0
votes
0
replies
45
views
tr2aacds error about class2pub
tr2aacds
class2pub
error
1 day ago by
380630938
• 0
0
votes
0
replies
60
views
analyze_diff_expr.pl result explanation
Trinity
analyze_diff_expr.pl
UP.subset
DEGs
1 day ago by
Roy.anupama11
• 0
1
vote
9
replies
1.4k
views
Fasterq-dump unexpected parameter error (unexpected parameter[256]: '/home/GEOdata/sra/SRR6687807.sra)
RNA-Seq
software error
updated 1 day ago by
ATpoint
61k • written 19 months ago by
cwliu0222
• 0
5
votes
5
replies
349
views
Should I wait for finishing the BWA MEM alignment?
Bwa
mem.
updated 1 day ago by
seidel
9.4k • written 1 day ago by
oğuzhan
• 0
0
votes
0
replies
91
views
CNEFinder merge chromosomes
chromosome
concatanate
CNEFinder
1 day ago by
kagan.ferenc
• 0
1
vote
1
reply
104
views
Demuxlet using Illumina GSA?
global
array
demuxlet
screening
gsa
updated 1 day ago by
cpad0112
20k • written 1 day ago by
kgoss
▴ 10
0
votes
0
replies
73
views
homer not configured properly
Homer
makeTagDirectory
1 day ago by
amahdi779
• 0
0
votes
5
replies
213
views
Subsetting Vcf based on CHROM and POSS
subsetting
vcfR
vcf
updated 1 day ago by
Pierre Lindenbaum
145k • written 2 days ago by
AndrMod
• 0
0
votes
3
replies
160
views
Soft-trim for multistep alignment?
alignment
sequencing
updated 1 day ago by
GenoMax
115k • written 2 days ago by
TheDurtlerTurtle
• 0
0
votes
0
replies
105
views
Infinium MethylationEPIC Annotation under hg38
Microarray
Methylation
2 days ago by
Molin
• 0
0
votes
1
reply
138
views
What LOH means in CANVAS
CANVAS
updated 1 day ago by
Carambakaracho
★ 3.0k • written 2 days ago by
ManuelDB
▴ 30
0
votes
0
replies
118
views
Understanding the output generated using rehh package
sfs
Rehh
2 days ago by
taniamahmood38
▴ 20
0
votes
2
replies
173
views
R: problem with running time-series analysis software: Mfuzz
mfuzz
time-series
replace
3 days ago by
soda
▴ 40
0
votes
1
reply
132
views
Running synteny of 2 strain.
Bioinformatics
updated 23 hours ago by
dthorbur
▴ 220 • written 3 days ago by
jhilimsikder.biotech
• 0
0
votes
2
replies
209
views
VCF file format for VCFTOOLs
plink
vcftools
vcf
updated 3 days ago by
Pierre Lindenbaum
145k • written 3 days ago by
syxsu
• 0
1
vote
3
replies
220
views
How to calculate percentage of chimeras from r1/r2 files
chimera
usearch
chimeric
paired-end-reads
sequences
updated 1 day ago by
Asaf
8.7k • written 3 days ago by
eli_bayat
▴ 60
1
vote
5
replies
215
views
Making a pheatmap legend with superscripts
pheatmap
updated 21 hours ago by
Ram
36k • written 3 days ago by
swbarnes2
12k
3
votes
7
replies
300
views
awk command merge files on one common column
Linux
shell-scripting
awk
updated 1 day ago by
zx8754
11k • written 3 days ago by
adyashapanda04
▴ 10
1
vote
2
replies
188
views
Why am I getting same linear regression lines for 'x' on 'y' and 'y' on 'x'?
lm
regression
linear
offtopic
updated 3 days ago by
karl.stamm
4.0k • written 3 days ago by
glyptonotus
• 0
1
vote
2
replies
212
views
Inflation in Imputed data
genomic
immunochip
inflation
topmed
3 days ago by
desicasares@gmail.com
▴ 10
1
vote
2
replies
193
views
Multi Alignment - How to deal with uncertainty?
alignment
transcriptomics
RNASeq
2 days ago by
andrebolerbarros
• 0
1
vote
3
replies
196
views
How to deal with different transcripts ID between versions
gencode
ensembl
updated 3 days ago by
Ram
36k • written 3 days ago by
Manuel
• 0
1,000 results • Page
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A: EdgeR analysis with CPM normalzed counts
Comment: PC build for Nanopore data analysis
Comment: PC build for Nanopore data analysis
Answer: PC build for Nanopore data analysis
Answer: PC build for Nanopore data analysis
Comment: DESeq2 and WGCNA
A: How To Interpret Breakdancer Output File ?
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Answer: Biopython intron-exon boundary nucleotide frequencies
by
Joe
20k
Eukaryote genomics is not a area of expertise for me so apologies if I miss some subtlety with the exons/introns here, but if the tasks is …
Comment: BED file from GSEA gene set
by
ATpoint
61k
What exactly is the question? Do you need code to make a BED file, and if so based on what? Gene symbols, coordinates of peaks? Please add …
Comment: Strange Trimmomatic behavior
by
lieven.sterck
13k
can you first confirm it is GBS data we're talking about here?
Comment: arrange samples in same order in rows and column in R
by
Bioinfonext
▴ 380
This also shows error, Is there any way in R to arrange samples in same rows/column? fit <- lmFit(t(mval), var) Error in lmFit(t(mval),…
Comment: PC build for Nanopore data analysis
by
Jean-Karim Heriche
25k
I assumed that this was already covered because of the mention of > a pipeline for the data that is subsequently generated
Answer: PC build for Nanopore data analysis
by
GenoMax
115k
I assume you are referring to MinION sequencing since other larger ONT sequencers are supplied with built in compute for doing some of the …
Comment: PC build for Nanopore data analysis
by
GenoMax
115k
ONT basecallers are [**performant only with GPU**][1]'s. [1]: https://hackmd.io/@Miles/B1U-cOMyu#GPUs-and-Guppy-base-calling
Comment: bcftools stats: definition of indel type
by
WouterDeCoster
46k
But it requires that there is a match between a part of the REF allele and a part of the ALT allele (https://github.com/samtools/htslib/blo…
Comment: bcftools stats: definition of indel type
by
Pierre Lindenbaum
145k
// i and j are the position in the alt and ref string if ( a[i]!=END_OF_STRING && r[j]==END_OF-STRING ) { …
Comment: bcftools stats: definition of indel type
by
Pierre Lindenbaum
145k
so looking quickly an indel is when this is not a symbolic allele (<BND>) and the length of REF and the current ALT are not the same.
Comment: bcftools stats: definition of indel type
by
WouterDeCoster
46k
Yes, but I cannot figure out in which cases the INDEL type is assigned: ``` if ( *a && !*r ) { if ( *a==']' || *a=='[' ) { …
Answer: MG RAST for Eukaryota
by
young_bioinformatician
▴ 170
Hi Tom, Yes, you can go with the predicted proteins for the annotation/downstream analysis.
Comment: bcftools stats: definition of indel type
by
Pierre Lindenbaum
145k
if the type hasn't been already defined, the type is set as an array of bytes using `OR` and this function: https://github.com/samtools/hts…
Comment: arrange samples in same order in rows and column in R
by
Kevin Blighe
81k
You probably just need: fit <- lmFit(t(mval), var) In your model, you are also attempting to adjust for a lot of covariates- is that…
Comment: arrange samples in same order in rows and column in R
by
Bioinfonext
▴ 380
Thank Basti, I already did this, could you please above posted full code? Many thanks,
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