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60 results • Page
1 of 2
Sort: replies
Rank
Views
Votes
Replies
18
votes
31
replies
5.7k
views
How can I easily remove overlapping transcripts, keeping only longest transcript, in a GFF file.
gff
parse
updated 17 hours ago by
Juke34
7.8k • written 4.5 years ago by
a.rex
▴ 350
8
votes
10
replies
530
views
7 follow
Snakemake vs Nextflow Upcoming bioinformatics Project
Programming
Masters
updated 9 hours ago by
cfos4698
▴ 720 • written 8 days ago by
rackbersingh
• 0
6
votes
9
replies
6.7k
views
8 follow
Any methods available to do QC analysis of Pacbio raw data??
Assembly
genome
Pacbio
next-gen
sequencing
updated 18 hours ago by
Afif Elghraoui
• 0 • written 5.5 years ago by
karthic
▴ 120
12
votes
9
replies
684
views
6 follow
How to find promoter sequence of a gene?
promoter
17 hours ago by
sunyeping
▴ 80
7
votes
8
replies
678
views
Aberrant splicing in bulk RNAseq
aberrant-splicing
transcript
isoform
exon
3 hours ago by
txema.heredia
▴ 70
7
votes
7
replies
484
views
Nextflow rnaseq finishing early
RNA-seq
nextflow
updated 21 hours ago by
Ram
38k • written 22 hours ago by
Raygozak
★ 1.4k
6
votes
7
replies
1.2k
views
Extract CDS from maker gff
CDS
maker2
annotation
gff
updated 18 hours ago by
lieven.sterck
14k • written 21 months ago by
Sarah
▴ 60
5
votes
7
replies
359
views
Most efficient way to run Diamond against a very very large database (i.e., NCBI's NR)?
protein
annotation
alignment
diamond
nr
19 hours ago by
O.rka
▴ 650
3
votes
6
replies
314
views
How to demultiplex single end - dual index run - NextSeq 500
sequencing
bcl2fastq
rna-seq
updated 2 hours ago by
GenoMax
127k • written 4 days ago by
Apex92
▴ 260
3
votes
6
replies
397
views
ClusterProfiler enrichKEGG – remove organism name in plots?
KEGG
ggplot2
enrichKEGG
ClusterProfiler
updated 21 hours ago by
jv
★ 1.0k • written 7 days ago by
Sian
▴ 20
6
votes
6
replies
2.4k
views
Sites for Computer Aided Drug Designing
CADD
Simulations
in-silico
Docking
updated 4 hours ago by
contact
• 0 • written 8.2 years ago by
ruchikabhat31
▴ 60
0
votes
5
replies
232
views
featureCounts problem in reading Gff
featureCounts
GFF
RNA-seq
updated 16 hours ago by
Ram
38k • written 19 hours ago by
Beatrice
• 0
2
votes
5
replies
1.3k
views
Error building snpEff database "Transcript 'hypothetical_protein' already exists"
snpeff
database
build
updated 14 hours ago by
Jane
• 0 • written 4.7 years ago by
Lina F
▴ 200
0
votes
5
replies
334
views
Kallisto bustools for scRNA-seq
Kallisto
3 hours ago by
t.ru
▴ 20
0
votes
4
replies
332
views
RNA Sequencing and Vg pan -transcriptome build
fasta
pan-transcriptome
pan-genome
vg
17 hours ago by
kcarery
• 0
1
vote
4
replies
199
views
bash command to process a line
linux
command
updated 16 hours ago by
GenoMax
127k • written 17 hours ago by
saadleeshehreen
▴ 110
0
votes
4
replies
899
views
activity of unloaded/unassembled Tn5
sequencing
next-gen
updated 21 hours ago by
ATpoint
70k • written 5.1 years ago by
zhaohainancau
• 0
1
vote
4
replies
199
views
Artificial reads - remove multiple mapped reads against reference genome, and only keep reads that completely match without any mismatches - samtools
samtools
2 hours ago by
Agamemnon
▴ 60
3
votes
4
replies
275
views
differential gene analysis
DGE
2 hours ago by
kalyani
• 0
1
vote
4
replies
168
views
Centromere and telomere positions for Chm13v2 assembly
centromere
chm13v2
18 hours ago by
arsala521
▴ 10
2
votes
3
replies
252
views
How to get gene from PSIBLAST resuts
blast
homologous
psiblast
updated 18 hours ago by
lieven.sterck
14k • written 5 days ago by
Tom
• 0
1
vote
3
replies
77
views
merge vcf.gz file
vcf.gz
bcftools
2 hours ago by
Mali
• 0
3
votes
3
replies
222
views
Editing fasta headers
fasta
updated 22 hours ago by
Ram
38k • written 1 day ago by
Zoe
• 0
0
votes
3
replies
623
views
database on patients treated with CAR T-cell therapies
cancer
updated 4 hours ago by
contact
• 0 • written 16 months ago by
yueli7
▴ 240
0
votes
3
replies
82
views
GO enrichment analysis
enrichment
analysis
GO
updated just now by
Antonio R. Franco
★ 5.0k • written 3 hours ago by
hellokwmin
• 0
1
vote
3
replies
113
views
mpileup to sync file
AF
samtools
selection
vcf
popoolation
updated 4 hours ago by
Pierre Lindenbaum
153k • written 4 hours ago by
qstefano
▴ 20
0
votes
2
replies
257
views
Which GPU for local Colabfold
GPU
Alphafold
updated 2 hours ago by
matt_arnold_bio
• 0 • written 4 months ago by
Arjen Ten Have
▴ 360
0
votes
2
replies
321
views
Understanding multifactor designs and control variables in DESeq2
RNA-seq
DESeq2
18 hours ago by
kldsajf;ldsj;l
• 0
2
votes
2
replies
131
views
Retrieve hgnc_symbol from XM_ refseqs using BiomaRt
refseq_mrna_predicted
biomaRt
refseq
XM
6 hours ago by
ladina.hoesli
• 0
0
votes
2
replies
109
views
genome annotation [sstart] [send] - how to get protein sequence from gene
genome
annotation
2 hours ago by
danfarkas
• 0
2
votes
2
replies
73
views
STAR solo set parameters for scrna-seq
solo
STAR
2 hours ago by
t.ru
▴ 20
0
votes
2
replies
2.6k
views
demultiplexing with guppy_basecaller and guppy_barcoder using --detect_mid_strand_adapter --detect_mid_strand_barcodes produce > 90% of unclassified …
demultiplexing
guppy
21 minutes ago by
andres.firrincieli
3.1k
0
votes
1
reply
49
views
heatmap issue
heatmap
DESeq2
updated 2 hours ago by
yura.grabovska
▴ 50 • written 2 hours ago by
kalyani
• 0
0
votes
1
reply
77
views
syntax errors when running part3 all-against-all
error
AssertDatabaseVersionsInSync
syntax
all-against-all
updated 22 hours ago by
Ram
38k • written 22 hours ago by
Sofia
• 0
0
votes
1
reply
60
views
boxplot issue
Boxplot
DESeq2
2 hours ago by
kalyani
• 0
0
votes
1
reply
166
views
Variant caller reports a homozygous variant genotype, but more reads are associated with reference
bcftools
variants
updated 5 hours ago by
colindaven
4.6k • written 1 day ago by
rebeliscu
▴ 50
0
votes
1
reply
84
views
Is it possible to use pseudoalignments.bam to run rMATs?
Kallisto
rMATs
updated 10 hours ago by
dsull
★ 4.0k • written 11 hours ago by
Lillian
• 0
1
vote
1
reply
109
views
When to merge multiple fastq files into one for RNAseq analysis?
rnaseq
aligning
bowtie2
updated 12 hours ago by
GenoMax
127k • written 13 hours ago by
lunarskye222
• 0
0
votes
1
reply
89
views
Snakemake doesn't recognize output files even though they are created
python
Snakemake
updated 5 hours ago by
Shred
★ 1.0k • written 7 hours ago by
DdogBoss
• 0
0
votes
1
reply
75
views
installation of Snapgene tool in Ubuntu
installation
snapgene
Ubuntu
updated 4 hours ago by
ATpoint
70k • written 4 hours ago by
Fizzah
▴ 20
0
votes
1
reply
112
views
Time change in expression vs time change in phenotype
RNA-Seq
DGE
DESeq2
10 hours ago by
Ivan
• 0
0
votes
1
reply
82
views
Total No of Genes of GENCODE Release 43
gene
numbers
updated 3 hours ago by
ATpoint
70k • written 11 hours ago by
ahmad
• 0
0
votes
1
reply
34
views
Dealing with very large gene-lists in GSEA
R
fgsea
GSEA
updated 25 minutes ago by
Trivas
▴ 710 • written 2 hours ago by
yura.grabovska
▴ 50
1
vote
0
replies
98
views
Herald:
The Biostar Herald for Tuesday, March 28, 2023
herald
23 hours ago by
Biostar
1.6k
0
votes
0
replies
116
views
how can we improve genome assembly levels ? from contig to complete using bioinformatics pipelines?
contig
genome
pipelines
assembly
updated 22 hours ago by
Ram
38k • written 1 day ago by
vasudhapai
• 0
0
votes
0
replies
12
views
i need to update MitoZ 3.4 to 3.5
mit0Z
assembly
tool
1 hour ago by
manaswiniparija3
▴ 10
0
votes
0
replies
112
views
How to export GWAS lists available in Open Targets database
GWAS
gene
openTargets
1 hour ago by
dzisis1986
▴ 60
0
votes
0
replies
61
views
Diffbind: how to get raw read counts and normalized read counts
Diffbind
rawcount
9 hours ago by
soda
▴ 40
0
votes
0
replies
54
views
GO analysis using diamond blastp output
blastp
GO
analysis
Diamond
7 hours ago by
hellokwmin
• 0
0
votes
0
replies
123
views
News:
The Canadian Bioinformatics Workshops are back for summer 2023
CBW
training
workshop
19 hours ago by
bioinformatics.ca
• 0
60 results • Page
1 of 2
Recent Votes
A: Extract Base Based On Position From Bam File
PyComplexHeatmap: a Python package to visualize multimodal genomics data
pulling snps from vcf file using ids
A: pulling snps from vcf file using ids
Answer: Scaling RNA-Seq data before clustering?
Answer: How to use CAFE from Orthofinder Results
Answer: merge vcf.gz file
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Recent Replies
Comment: GO enrichment analysis
by
Antonio R. Franco
★ 5.0k
I had the same situation that I solved using the R package TopGO. You have already the list of GO terms. Need to follow the instructions i…
Comment: demultiplexing with guppy_basecaller and guppy_barcoder using --detect_mid_stran
by
andres.firrincieli
3.1k
Hi @6f8262bb I still have no idea what could be the cause but switching to guppy v6.2 solved this problem
Answer: Dealing with very large gene-lists in GSEA
by
Trivas
▴ 710
IMO, in those cases you could look at ES instead of NES. Regardless, within the function `fgsea`, you can set the parameters `minSize` and …
Comment: merge vcf.gz file
by
Mali
• 0
file1 = '/sci/labs/orzuk/orzuk/projects/Skin/data/Ichilov/vcfFiles/vcfFiles/eb3_1001_748-gatk-haplotype.final.vcf.gz' file2 = '/sci/labs/or…
Comment: Which GPU for local Colabfold
by
matt_arnold_bio
• 0
Another giveaway is that when you hit run, it will say either "Running on GPU" or "Running on CPU" in the log output... ![enter image desc…
Answer: Which GPU for local Colabfold
by
matt_arnold_bio
• 0
Hi Arjen, This is a little while ago now so maybe this is not that helpful but... You should be able to tell if the GPU is being seen…
Comment: STAR solo set parameters for scrna-seq
by
t.ru
▴ 20
it's single cell mars-seq. Yes sorry its a fastq file.
Answer: boxplot issue
by
yura.grabovska
▴ 50
First of all, you're not outputting the result of your scale to anything... t(apply(mat, 1, scale)) colnames(mat) <- rownames(cold…
Comment: STAR solo set parameters for scrna-seq
by
GenoMax
127k
> a fasta file similar to this This is not a fasta file It is a fastq format file. Are you sure this is single cell RNAseq data? Looking…
Answer: heatmap issue
by
yura.grabovska
▴ 50
Your controls clearly show variable expression for the genes you're plotting so to get them to stick together on the left, you would need t…
Comment: How to demultiplex single end - dual index run - NextSeq 500
by
GenoMax
127k
Correct. This is a single-end dual indexed (8 bp each) run.
Comment: genome annotation [sstart] [send] - how to get protein sequence from gene
by
danfarkas
• 0
Hi shenwei356, Thanks for the clarification. However, I did try this, and it was not yielding the expected amino acid sequences. This is w…
Comment: Artificial reads - remove multiple mapped reads against reference genome, and on
by
Agamemnon
▴ 60
I ran ```samtools view -F 4 -q 42 test.bam | wc -l``` and I get ```6159141```, why is there a discrepancy, as originally only ```5200484```…
Comment: differential gene analysis
by
kalyani
• 0
okay thankks!
Comment: Kallisto bustools for scRNA-seq
by
t.ru
▴ 20
@SRR17050039.1 NB501465:544:HF2H7BGXB:1:22104:14442:1233_TCCTGAGC_barcode=NA-EEEE-AAAAAEE-EEEEEEEE-GCTG-TGCCAGA-ACGTTCAT-W202012/1 GCCCTGTA…
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