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1,000 results • Page
1 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
14
views
Snakemake doesn't recognize output files even though they are created
python
Snakemake
1 hour ago by
DdogBoss
• 0
0
votes
0
replies
12
views
GO analysis using diamond blastp output
blastp
GO
analysis
Diamond
1 hour ago by
hellokwmin
• 0
0
votes
0
replies
33
views
Diffbind: how to get raw read counts and normalized read counts
Diffbind
rawcount
4 hours ago by
soda
▴ 40
0
votes
0
replies
41
views
Total No of Genes of GENCODE Release 43
gene
numbers
6 hours ago by
ahmad
• 0
0
votes
0
replies
50
views
Error at phase 4 when running GeMoMa (homology-based annotation)
Homology
GeMoMa
Annotation
Genome
9 hours ago by
breannar
• 0
0
votes
0
replies
63
views
Passing strings for password, email authentication and download link
bash
datasets
curl
download
9 hours ago by
pr2009
▴ 10
0
votes
5
replies
209
views
featureCounts problem in reading Gff
featureCounts
GFF
RNA-seq
updated 11 hours ago by
Ram
38k • written 14 hours ago by
Beatrice
• 0
0
votes
1
reply
105
views
Time change in expression vs time change in phenotype
RNA-Seq
DGE
DESeq2
5 hours ago by
Ivan
• 0
0
votes
0
replies
58
views
How to perform a gsva assessing for the directonality of the genes.
gsva
16 hours ago by
roybatty269
• 0
7
votes
7
replies
466
views
Nextflow rnaseq finishing early
RNA-seq
nextflow
updated 15 hours ago by
Ram
38k • written 17 hours ago by
Raygozak
★ 1.4k
0
votes
1
reply
70
views
syntax errors when running part3 all-against-all
error
AssertDatabaseVersionsInSync
syntax
all-against-all
updated 17 hours ago by
Ram
38k • written 17 hours ago by
Sofia
• 0
0
votes
0
replies
64
views
calculation of calibration factors using impuation reference panel and ethnicity
GWAS
Calibration
factor
18 hours ago by
parveenkayenat
• 0
1
vote
3
replies
170
views
Artificial reads - remove multiple mapped reads against reference genome, and only keep reads that completely match without any mismatches - samtools
samtools
updated 18 hours ago by
GenoMax
127k • written 19 hours ago by
Agamemnon
▴ 60
0
votes
0
replies
67
views
Haploview linkage format .ped and .info file error
plink
Haploview
vcftool
19 hours ago by
Nai
▴ 50
0
votes
1
reply
77
views
Clustering with monocle 3
scRNA-seq
trajectory
analysis
updated just now by
fracarb8
▴ 940 • written 19 hours ago by
Eisuan
▴ 20
0
votes
0
replies
96
views
How to export GWAS lists available in Open Targets database
GWAS
phenotype
openTargets
gene
21 hours ago by
dzisis1986
▴ 60
0
votes
0
replies
103
views
Bcftools consensus generates mismatched consensus sequence
Consensus
sequence
22 hours ago by
Duy
• 0
0
votes
0
replies
70
views
Is there a function to get the number of aligned sites between pairs of sequences in a multiple sequence alignment in R?
msa
R
22 hours ago by
audrey
• 0
0
votes
0
replies
92
views
Nucleotide substitution model and neighbor-joining tree
phylogeny
substitution
mega
neighbor-joining
modeltest
22 hours ago by
poecile.pal
▴ 50
0
votes
0
replies
94
views
Octopus advanced vcf guide: Example of overlapping vcf calls with *
vcf
spanning
alleles
octopus
8 hours ago by
penington.j
• 0
0
votes
0
replies
110
views
how can we improve genome assembly levels ? from contig to complete using bioinformatics pipelines?
contig
genome
pipelines
assembly
updated 16 hours ago by
Ram
38k • written 1 day ago by
vasudhapai
• 0
0
votes
0
replies
121
views
Link products to their genes
RNA-SEQ
GO
edgeR
1 day ago by
Pegasus
▴ 80
0
votes
0
replies
116
views
Trajectory analysis using Monocle3 with Seurat sub-clustering
scRNA-seq
Trajectory
Seurat
analysis
Monocle3
1 day ago by
joonhong kwon
▴ 40
0
votes
1
reply
168
views
Error parsing strand (?) from GFF line
assembly
updated 1 day ago by
cmdcolin
★ 2.9k • written 1 day ago by
hafiz.talhamalik
▴ 350
0
votes
0
replies
106
views
Variant caller reports a homozygous variant genotype, but more reads are associated with reference
bcftools
variants
1 day ago by
rebeliscu
▴ 50
1
vote
0
replies
134
views
List of Ongoing and Planned Long Read Sequencing studies?
long-read-sequencing
third-generation
updated 1 day ago by
Ram
38k • written 1 day ago by
Vincent Laufer
★ 2.5k
0
votes
1
reply
152
views
SNP ID (rsID) to Chr no. and Position
Annotation
1 day ago by
Jewahir
• 0
0
votes
0
replies
123
views
how to plot distribution of SNPs across a set of genes based on distance between snp and gene
snp
genes
updated 1 day ago by
Ram
38k • written 1 day ago by
rheab1230
▴ 140
0
votes
0
replies
106
views
Reactome Species Comparison - analysis table
reactome
20 hours ago by
a11msp
▴ 120
0
votes
1
reply
147
views
Using multimaping reads or unique reads on featurecounts?
featurecounts
HISAT2
updated 1 day ago by
GenoMax
127k • written 1 day ago by
omargmc.tak
• 0
0
votes
0
replies
97
views
How to import impute2.dosage files to analyse it in R (GWAS)
regression
GWAS
impute2
dosage
1 day ago by
Sebastian
• 0
0
votes
0
replies
97
views
Michigan Imputation server failed job
michigan-imputation-server
vcf
updated 1 day ago by
Ram
38k • written 1 day ago by
Najla
• 0
0
votes
0
replies
96
views
MD simulation error
MD
schrodinger
updated 1 day ago by
Ram
38k • written 1 day ago by
mixmatchey
• 0
0
votes
0
replies
102
views
File has zero value indivuals
Haploview
updated 1 day ago by
Ram
38k • written 1 day ago by
Nai
▴ 50
0
votes
4
replies
305
views
Kallisto bustools for scRNA-seq
Kallisto
updated 8 hours ago by
dsull
★ 4.0k • written 1 day ago by
t.ru
• 0
0
votes
0
replies
126
views
KEGGList Error in R
KEGGList
1 day ago by
GiV17
▴ 50
0
votes
0
replies
119
views
GATK VariantAnnotator -A PossibleDeNovo
VariantAnnotator
GATK
1 day ago by
zihanss
• 0
0
votes
4
replies
731
views
MapSplice2 gives error if the thread count (-p value) is greater than 2
Mapsplice2
fusion_candidates
updated 1 day ago by
GenoMax
127k • written 20 months ago by
nkmalini97
• 0
0
votes
0
replies
118
views
TrN (df = k+5) and TrNe (df = k+2) - which of these Tamura-Nei model variants is used in MEGAx?
Tamura-Nei
phylogeny
phangorn
modelTest
mega
2 days ago by
poecile.pal
▴ 50
0
votes
0
replies
180
views
How to sort graph based on fold change and instead of activated and suppressed, how to add up and downregulated in graph header?
clusterprofiler
2 days ago by
sharmatina189059
▴ 110
1
vote
4
replies
252
views
Protein name in GenBank
genbank
python
biopython
updated 2 days ago by
GenoMax
127k • written 2 days ago by
Daniel
• 0
0
votes
1
reply
183
views
doing PBS(population branch statistics) in ANGSD
fst
pbs
ANGSD
18 hours ago by
Blessing
• 0
0
votes
1
reply
170
views
Tell me about making a transcriptome model of a specific tissue.
model
transcriptome
updated 2 days ago by
ATpoint
70k • written 2 days ago by
Soliloquy
▴ 10
0
votes
0
replies
166
views
How to fix FreeBayes error "unable to find FASTA index entry for bed files"
calling
freebayes
variant
RNA-Seq
2 days ago by
wlei091226
• 0
0
votes
1
reply
192
views
how to import hdf5 Hi-C data into R using HiTC package
hdf5
importC
R
HiTC
updated 3 days ago by
rpolicastro
11k • written 3 days ago by
rheab1230
▴ 140
0
votes
0
replies
157
views
Emapplot Pie Graphic Legend Interferes with Map
enrichplot
clusterprofiler
Emapplot
3 days ago by
raquel.ajalik
• 0
1
vote
0
replies
162
views
Minimap2 giving opposite strand orientation than Pychopper
nanopore
Pychopper
Minimap2
3 days ago by
vanda.gaonach-lovejoy
▴ 10
0
votes
4
replies
327
views
RNA Sequencing and Vg pan -transcriptome build
fasta
pan-transcriptome
pan-genome
vg
11 hours ago by
kcarery
• 0
0
votes
0
replies
158
views
What is the meaning of 'a too large, ITMAX too small in gamma countinued fraction (gcf)'
meta
analysis
GWAS
METAL
updated 3 days ago by
GenoMax
127k • written 3 days ago by
ymberzal
• 0
0
votes
4
replies
389
views
Problem with fatsq-dump
fastq-dump
sratoolkit
2 days ago by
Utpal
• 0
1,000 results • Page
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Recent Votes
Answer: Snakemake vs Nextflow Upcoming bioinformatics Project
Answer: Retrieve hgnc_symbol from XM_ refseqs using BiomaRt
Answer: Retrieve hgnc_symbol from XM_ refseqs using BiomaRt
Answer: What is the difference between agilent_wholegenome and agilent_wholegenome_4x44k
Answer: What is the difference between agilent_wholegenome and agilent_wholegenome_4x44k
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
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Recent Replies
Answer: demultiplexing with guppy_basecaller and guppy_barcoder using --detect_mid_stran
by
Yuri
• 0
Hi @and did you ever figure out why guppy was resulting in 90% of reads in unclassified folder? I am running into the same issue, and am…
Comment: Retrieve hgnc_symbol from XM_ refseqs using BiomaRt
by
ladina.hoesli
• 0
Thank you very much, this helps a lot!
Answer: Snakemake vs Nextflow Upcoming bioinformatics Project
by
cfos4698
▴ 720
There are a lot of votes for Nextflow here, and it's generally pretty popular (and increasing in popularity). As a 'dissenting' voice, I'll…
Answer: Is it possible to use pseudoalignments.bam to run rMATs?
by
dsull
★ 4.0k
No, you can't do that with kallisto's bam files. For one, kallisto (by default) doesn't map to introns which is required by rMATs. You c…
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by
shenwei356
8.0k
It means that the gene is on the negative/minus strand. So you need to compute the reverse complementary sequence before translating it to …
Answer: When to merge multiple fastq files into one for RNAseq analysis?
by
GenoMax
127k
As long as the sample name matches across the lanes they are pieces of the same sample. > I was thinking of combining the two fastq files…
Comment: Kallisto bustools for scRNA-seq
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dsull
★ 4.0k
Yes, just put that fastq file (it'll be the same as any other kallisto bustools run, except you have just one fastq file and you have that …
Comment: Error building snpEff database "Transcript 'hypothetical_protein' already exist
by
Jane
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Hi, I have the same issue. After running the command, I run the "sh scripts/buildDbNcbi.sh U00096.2" to download again. Then the same issu…
Comment: bash command to process a line
by
saadleeshehreen
▴ 110
Thanks a lot. It worked
Answer: bash command to process a line
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127k
With just one line example not sure if this will work awk -F '[|_]' '{print $2,$4}' your_file CU459141.1 CAM87240.1
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by
kcarery
• 0
Thank you! I found this as well and trying to understand it now.
Comment: RNA Sequencing and Vg pan -transcriptome build
by
kcarery
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Thank you so much! This is where I am leading back to as well! I don't have much insights into Hisat2. I am going to give it a go this week…
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by
Juke34
7.8k
Interesting, why would you merge genes that are on different strands? They should be different genes. It cannot be done without modifying t…
Comment: featureCounts problem in reading Gff
by
Beatrice
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That's the output, so apparently I have the exon. Anyway, after running grep command the featureCounts worked, even though I didn't change …
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saadleeshehreen
▴ 110
Yes the word start with lcl| and always sperated by _prot_. I am very naive pattern matching and extraction. I was trying to cut the field …
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