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812 results • Page
2 of 17
Sort: replies
Rank
Views
Votes
Replies
16
votes
8
replies
290
views
Tool:
ChatGPT optimized for bioinformatics questions
gpt
3 hours ago by
Sasha
▴ 280
4
votes
8
replies
771
views
VEP tab/vcf - Different output
VEP
ensembl
updated 1 day ago by
Ben_Ensembl
★ 2.2k • written 14 months ago by
Filago
▴ 90
2
votes
7
replies
514
views
What is "pident" (percentage of identical matches) in the "Diamond" protein alignment ?
protein
alignment
updated 4 days ago by
Vincent Laufer
★ 2.9k • written 5 days ago by
Alexander
▴ 70
1
vote
7
replies
333
views
How GATK pipeline called a homozygeous alternate allele (1/1) although one copy is supported by 0 reads ?
SNP
GATK
updated 5 days ago by
Ram
39k • written 6 days ago by
mohsamir2016
▴ 30
3
votes
7
replies
1.1k
views
Find 3'UTRs for species
Assembly
alignment
updated 5 days ago by
Ram
39k • written 3.8 years ago by
Palgrave
▴ 110
2
votes
7
replies
897
views
Forum:
Future prospects: NGS vs Gene editing (using CRISPR CAS9, AAVs and similar methods)
NGS
CRISPR-Cas9
updated 2 days ago by
Ram
39k • written 3.7 years ago by
Gabriel
▴ 120
6
votes
7
replies
358
views
NCBI API, Perl
API
NCBI
updated 2 days ago by
GenoMax
130k • written 2 days ago by
alessandro.alma00
• 0
0
votes
7
replies
559
views
Why are some WES VCFs larger than others?
WES
sequencing
genomics
NGS
exome
2 days ago by
Kermit
▴ 80
3
votes
7
replies
4.2k
views
Getting Pairwise Sequence Alignment Score With Biopython
biopython
alignment
clustalw
updated 1 day ago by
Jonathan Lefebre
▴ 70 • written 11.5 years ago by
Lakshmi
• 0
8
votes
7
replies
1.1k
views
Forum:
Is it okay to pool sample for RNAseq and proteomics study?
RNA-Seq
updated 1 day ago by
Ram
39k • written 3.5 years ago by
sha_6p
▴ 10
1
vote
7
replies
2.7k
views
RGT TypeError: unsupported operand type(s) for +: 'NoneType' and 'int'
RGT
TF-footprinting
ATAC-seq
updated 3 hours ago by
Ram
39k • written 4.5 years ago by
grant.hovhannisyan
★ 2.5k
10
votes
7
replies
1.5k
views
Forum:
Is trimming always better?
RNA-Seq
QC
trimmomatic
trimming
updated 6 days ago by
Ram
39k • written 4.0 years ago by
Mozart
▴ 330
5
votes
7
replies
1.7k
views
How to prevent reduce from being performed in GRanges during setdiff
blunt-end
genomicranges
setdiff
updated 5 days ago by
hossiny
• 0 • written 2.3 years ago by
Bosberg
▴ 50
8
votes
7
replies
391
views
including samples for which group is unknown to help adjust for another variable
TCGA
design
RNA-Seq
deseq2
updated 6 days ago by
Vincent Laufer
★ 2.9k • written 7 days ago by
pilargmarch
▴ 100
11
votes
7
replies
5.1k
views
Forum:
Using Graphics Processing Units (GPUs) in bioinformatics
algorithm
GPU
updated 5 days ago by
Ram
39k • written 3.8 years ago by
Denis
▴ 270
8
votes
7
replies
1.2k
views
Polygenic Risk Score analysis
PRS
GWAS
updated 2 days ago by
Ram
39k • written 3.6 years ago by
pedro.raposo3
▴ 20
4
votes
7
replies
2.2k
views
low bootstrap value?
phylogeny
genome
alignment
updated 6 days ago by
Ram
39k • written 4.0 years ago by
Kumar
▴ 100
3
votes
7
replies
442
views
How to sort gff3 according to chromosome order?
gff3
sort
updated 4 days ago by
Pierre Lindenbaum
154k • written 5 days ago by
BioinfoBee
• 0
1
vote
7
replies
1.9k
views
Job:
PhD scholarship in Bioinformatics, Rostock University Medical Center (Rostock, Germany)
PhD
scholarship
updated 2 hours ago by
Ram
39k • written 3.3 years ago by
Israel Barrantes
▴ 790
0
votes
6
replies
380
views
Impute haplotypes (ImputePipelinePlugin) execution error - PHG
phg
2 days ago by
jrodrigu
• 0
7
votes
6
replies
2.8k
views
Error: --fst requires at least two nonempty clusters.
Plink
updated 2 days ago by
dre.gaudio
• 0 • written 6.0 years ago by
msimmer92
▴ 300
4
votes
6
replies
2.4k
views
Forum:
NGS Data Storage Best Practices (Clinical)
NGS
clinical
storage
updated 1 day ago by
Ram
39k • written 3.5 years ago by
Robert Sicko
▴ 630
3
votes
6
replies
2.0k
views
h5ad cellxgene to R
single-cell
h5
cellxgene
anndata
R
updated 3 days ago by
GenoMax
130k • written 6 months ago by
firestar
★ 1.5k
7
votes
6
replies
315
views
Italicise annotations with pheatmap
R
Pheatmap
updated 1 day ago by
ATpoint
72k • written 1 day ago by
jamie.pike
▴ 80
2
votes
6
replies
1.7k
views
How can I identify cells from Single cell experiment (SCE) using bulk RNA experiment (RNAseq) genes signatures?
RNA-Seq
next-gen
updated 5 days ago by
Ram
39k • written 3.8 years ago by
sofiagreen72211
▴ 30
10
votes
6
replies
1.1k
views
6 follow
Forum:
Pros and cons to do biomedical research in pharmaceutical company
industry
career
academia
updated 2 hours ago by
Ram
39k • written 3.3 years ago by
Shicheng Guo
★ 9.3k
1
vote
6
replies
722
views
ATAC seq Normalization and analysis pipeline problems
csaw
R
ATAC-seq
updated 3 hours ago by
Ram
39k • written 7 months ago by
bridgetaylward13
▴ 10
2
votes
6
replies
713
views
Forum:
Error in posting to Biostars?
meta
updated 5 hours ago by
Ram
39k • written 3.4 years ago by
vctrm67
▴ 40
1
vote
6
replies
572
views
Counting intronic reads in bulk RNA-seq
rna-seq
updated 5 days ago by
swbarnes2
13k • written 12 days ago by
John Ma
▴ 310
6
votes
6
replies
1.1k
views
Want read count with respect to geneID instead of transcript IDs
RNA-Seq
updated 1 day ago by
Ram
39k • written 3.6 years ago by
archana.bioinfo87
▴ 180
4
votes
6
replies
460
views
RNASeq gene labeling and mRNA filter from bulkRNA data.
RNA-Seq
RSubreads
1 hour ago by
Yeeshouw
• 0
0
votes
6
replies
309
views
Getting same value for start and end position, "DNA methylation"
DNAmethylation
methylkit
updated 1 day ago by
ATpoint
72k • written 2 days ago by
Pankaj
• 0
7
votes
6
replies
323
views
Contigs to chromosomes annotation
Assembly
mapping
contigs
updated 1 day ago by
GenoMax
130k • written 1 day ago by
alexandru.bologa.marian
▴ 50
0
votes
6
replies
339
views
variant allelic fraction
vep
updated 1 day ago by
Ram
39k • written 2 days ago by
Jom
• 0
2
votes
6
replies
329
views
Embryo transcriptome
database
transcriptome
SRA
updated 5 hours ago by
Basti
★ 1.6k • written 2 days ago by
firefox91
• 0
4
votes
6
replies
3.1k
views
convert gbk to fasta
genome
updated 4 hours ago by
Ram
39k • written 3.4 years ago by
wellinsantos84
▴ 10
4
votes
6
replies
319
views
Single Cell Rna Seq Using BD Rhapsody
Rhapsody
BD
updated 6 days ago by
Ram
39k • written 6 days ago by
abbas.waseem.gcu
▴ 20
5
votes
6
replies
433
views
How to calculate TPM from featureCounts output
rna-seq
TPM
featurecounts
13 hours ago by
survive
• 0
4
votes
6
replies
1.5k
views
Why weblogo of biopython doesn't work?
Biopython
Weblogo
updated 5 days ago by
minakshiboruahassam
• 0 • written 9 months ago by
Plus
▴ 20
4
votes
6
replies
384
views
calculate p value and associated z score for snp-gene pair
snp
association
gene
pvalue
20 hours ago by
rheab1230
▴ 140
2
votes
6
replies
646
views
How to identify the corresponding gene of a short sequence of a genome?
fasta
gene
genome
sequence
updated 1 day ago by
Ram
39k • written 3.5 years ago by
Kumar
▴ 100
2
votes
6
replies
513
views
Can I replace the single end sequenced sample with the failed pair end sequenced sample in RNAseq experiment?
RNA-Seq
sequencing
updated 1 hour ago by
Ram
39k • written 3.2 years ago by
doanphuong19
• 0
0
votes
6
replies
1.9k
views
Variable read length distribution after cutadapt running for my ATAC-seq datasets
cutadapt
read-length
alignment
ATAC-seq
updated 3 hours ago by
Ram
39k • written 3.1 years ago by
yaoyao20152031
• 0
7
votes
6
replies
1.4k
views
Forum:
Bioinformaticians - Am I on the Right Track?
Career
updated 1 day ago by
Ram
39k • written 3.5 years ago by
kstangline
▴ 70
7
votes
6
replies
1.1k
views
Job:
Come work with me! Bioinformatician - Boston MA
job
updated 3 days ago by
Joseph
• 0 • written 8 months ago by
Devon Ryan
103k
6
votes
5
replies
6.3k
views
Forum:
Converting GFF to GTF
GTF
GFF
updated 1 minute ago by
Ram
39k • written 3.2 years ago by
Juke34
7.9k
0
votes
5
replies
443
views
convert data frame with character column to data frame with integer column
r
updated 2 days ago by
Basti
★ 1.6k • written 5 days ago by
atemedorri137798
• 0
6
votes
5
replies
9.6k
views
Forum:
Single-end sequencing versus paired-end
Assembly
snp
sequencing
updated 3 hours ago by
Ram
39k • written 3.3 years ago by
Sujata
▴ 20
0
votes
5
replies
322
views
All combinations of two columns R
R
updated 5 days ago by
Ram
39k • written 5 days ago by
Fernando
• 0
3
votes
5
replies
2.1k
views
STAR genome generate taking long time and less thread.
RNA-Seq
STAR
updated 5 days ago by
Ram
39k • written 3.8 years ago by
Ranan Jyoti Sarma
▴ 70
812 results • Page
2 of 17
Recent Votes
Answer: Differences in GTF files hg19 and hg38
Answer: Saving results from yeastgenome.org blastp search
Answer: Saving results from yeastgenome.org blastp search
Comment: RNASeq gene labeling and mRNA filter from bulkRNA data.
Answer: Saving results from yeastgenome.org blastp search
Comment: snps from empty well, Illumina Sequencing
Extract sequences from a fastq file by a list of IDs
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Recent Awards •
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Scholar
to
GenoMax
130k
Popular Question
to
Payal
▴ 140
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to
nux
▴ 20
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Rory Stark
★ 1.8k
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Sasha
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v.berriosfarias
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Denis
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Recent Replies
Answer: Differences in GTF files hg19 and hg38
by
heureuse
• 0
Thank you very much. I get it from UCSC.
Comment: [python]sklearn.ensemble.RandomForestClassifier(TypeError: string indices must b
by
Arup Ghosh
3.2k
This post does not fit the theme of this forum.
Comment: CellRanger problem
by
Arup Ghosh
3.2k
Try with atleast 32 GB of Memory rather than 16 GB specified by `limitGenomeGenerateRAM` option.
Comment: Differences in GTF files hg19 and hg38
by
heureuse
• 0
Thank you very much. I get it from UCSC.
Comment: VCF file CSQ flag
by
Payal
▴ 140
Its a gvcf file #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S101 S102 S103 S104 S105
Comment: CellRanger problem
by
GenoMax
130k
And how much memory do you have assigned for this job? Likely you do not have enough memory for this process.
Comment: VCF file CSQ flag
by
Ram
39k
> a g.VCF file A `.vcf` file or a `gvcf` file?
Comment: CellRanger problem
by
Ram
39k
What is the cellranger command you're using?
Comment: RNASeq gene labeling and mRNA filter from bulkRNA data.
by
Yeeshouw
• 0
I see, I believe I was running an older version or have missed the option, I have updated to v2.10.5 and can see this option now. Thank you…
Answer: Saving results from yeastgenome.org blastp search
by
GenoMax
130k
Looks like yeastgenome site does not provide a way to export or save the results in any other format. You could do the search over at NCBI …
Answer: Differences in GTF files hg19 and hg38
by
GenoMax
130k
Not sure where you got your GTF for GRCh38 from but [**one from GENCODE**][1] has the level info you are looking for. chr1 HAVANA…
Comment: CHiP-Seq Questions
by
B.N.
• 0
Thank you for the suggestions Dr. Stark.
Comment: Diff Bind Questions
by
B.N.
• 0
Thank you so much for the insight Dr. Stark!
Comment: Is PanCan data microarray or rna-seq
by
GenoMax
130k
This particular example ("GeneChip") is an array. Early TCGA samples may have been done using arrays and later sequenced. Appears to be thi…
Comment: ChatGPT optimized for bioinformatics questions
by
Sasha
▴ 280
Hoping to add functionality around this. Stay tuned. Big problem for our space that needs to be resolved.
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