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600 results • Page
1 of 12
Sort: Votes
Rank
Views
Votes
Replies
12
votes
4
replies
504
views
Annotating TSS: By Transcript or by Gene? Code Validation Help Needed!
genome
bed
transcript
TSS
23 days ago by
Rafael Soler
★ 1.2k
10
votes
14
replies
3.8k
views
ATAC-seq data and deepTools: Small detail with impact on output
bigwig
read-length
deeptools
ATAC-seq
updated 2 hours ago by
Ram
39k • written 3.3 years ago by
gable_works
▴ 50
7
votes
7
replies
4.4k
views
RNA-Seq time series analysis using a DESeq2 spline approach yields far too many significant genes
splines
DESeq2
time-series
RNA-Seq
updated 8 days ago by
Ram
39k • written 4.4 years ago by
stu111538
▴ 80
7
votes
12
replies
888
views
Integrated genes from bulk RNA seq and ATAC seq
bulk-RNA
integrated
ATAC-seq
updated 13 days ago by
Sasha
▴ 280 • written 20 days ago by
Chris
▴ 100
6
votes
9
replies
968
views
Error when runing Bowtie2: (ERR): bowtie2-align exited with value 1
BAM
Bowtie
updated 26 days ago by
Ram
39k • written 4 months ago by
luzglongoria
▴ 40
6
votes
12
replies
601
views
Help with error in cellranger
Cellranger
updated 21 days ago by
GenoMax
130k • written 22 days ago by
Chris
▴ 100
6
votes
6
replies
584
views
On "wings" in volcano plots...
DEG
volcano
DGE
statistics
DE
updated 19 days ago by
ATpoint
72k • written 20 days ago by
kalavattam
▴ 120
6
votes
6
replies
2.7k
views
ChIP-Seq Intensity Analysis
R
ChIP-Seq
updated 20 days ago by
Ram
39k • written 5.5 years ago by
solveforj
▴ 20
6
votes
7
replies
1.4k
views
Bioinformatics Master Project With More Focus on Developing Algorithm and Software
Masters
Algorithm
Software
updated 26 days ago by
Ram
39k • written 6.0 years ago by
nilo
▴ 90
5
votes
7
replies
651
views
Are datasets for a unique cells, that downloded using sratoolkit?
RNA-Seq
sequencing
updated 17 days ago by
supernovamik
• 0 • written 3.4 years ago by
ee.mohseni.alert
▴ 50
5
votes
4
replies
1.5k
views
Detection of DE genes among different tissues of an organism during time - RNA seq
detection
DE-genes
multi-treatments
time-series
updated 8 days ago by
Ram
39k • written 6.9 years ago by
statfa
▴ 720
5
votes
7
replies
899
views
error while using cyvcf2 to parse the vcf file
cyvcf2
vcf
htslib
updated 26 days ago by
Ram
39k • written 12 months ago by
rheab1230
▴ 140
5
votes
5
replies
1.6k
views
bio-newbie / gene research / tools and methods
methods
research
gene
updated 19 days ago by
Ram
39k • written 5.4 years ago by
wizofe
• 0
4
votes
6
replies
545
views
How to pass from DNA to AA fasta
genetics
updated 16 days ago by
Buffo
★ 2.2k • written 19 days ago by
Anderson Stiward
• 0
4
votes
4
replies
294
views
Does adding reads cause batch effects?
kallisto
RNAseq
updated 5 days ago by
ATpoint
72k • written 6 days ago by
bioinfo
▴ 80
4
votes
8
replies
1.6k
views
How to extract promoter sequences from a plant draft genome?
promoter
genome
updated 4 days ago by
Ram
39k • written 3.7 years ago by
Kumar
▴ 100
4
votes
4
replies
360
views
Segmentation fault Biopython pairwise alignment
biopython
alignment
updated 8 days ago by
Joe
21k • written 12 days ago by
antoine.fauchois92
▴ 20
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
744
views
Open-Source software. Good or bad for the market?
genomic-analysis
software
updated 19 days ago by
Ram
39k • written 5.3 years ago by
Bioinformatician90
• 0
4
votes
8
replies
562
views
Error while running nf-core/rnaseq pipeline
nf-core
RNA-seq
15 days ago by
eesha28112001
• 0
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
4
votes
5
replies
1.2k
views
Distributed / parallel computing in bioinformatics
distributed-computing
updated 23 days ago by
Ram
39k • written 5.9 years ago by
CY
▴ 710
4
votes
6
replies
451
views
how to plot SV(structural variants) from many assemblies of a given locus
SV
21 days ago by
natalev
▴ 20
3
votes
9
replies
546
views
Estimate sizes of repeats in a especific Gene
CGG
Fragile-X
20 days ago by
Rafael
▴ 10
3
votes
2
replies
881
views
Creating a genotype matrix for BeviMed
snp
genome
Bayesian
updated 4 hours ago by
Ram
39k • written 3.4 years ago by
tacrolimus
▴ 110
3
votes
4
replies
2.4k
views
Unable to install Autogrid4
autogrid
software-error
autogrid4
updated 20 days ago by
Ram
39k • written 2.3 years ago by
roybatty269
• 0
3
votes
2
replies
579
views
STAR aligner FATAL ERROR not correct
fastq
star
updated 23 days ago by
Ram
39k • written 17 months ago by
Mike
▴ 10
3
votes
4
replies
1.3k
views
fastPHASE -F provided to estimate haplotype frequencies, but no freqs in output
genomics
phasing
fastPHASE
updated 16 days ago by
Ram
39k • written 5.2 years ago by
lakemonster
▴ 10
3
votes
6
replies
1.8k
views
Biopython TimeExceptionError how to handle?
biopython
entrez
updated 21 days ago by
Ram
39k • written 5.6 years ago by
Xylanaser
▴ 80
3
votes
1
reply
263
views
chromosome location to gene name and aa change
variant-annotation
17 days ago by
Zi
• 0
3
votes
4
replies
226
views
retaining only the clusters of interest
seurat
single-cell
scRna-seq
updated 5 hours ago by
Ram
39k • written 1 day ago by
shamza
• 0
3
votes
5
replies
362
views
Uniprot API access to download .pdb files
PDB
API
Python
Uniprot
13 days ago by
jdrohan
• 0
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
3
votes
5
replies
1.3k
views
Trouble with best practices
samtools
WES
NGS
GATK
updated 19 days ago by
Ram
39k • written 5.3 years ago by
erarroji
• 0
3
votes
8
replies
1.7k
views
What is the minimum system requement for oxford nanopore read assembly
Assembly
updated 13 days ago by
Ram
39k • written 4.6 years ago by
nagendranp1991
• 0
3
votes
12
replies
2.2k
views
What is NCBI Gene ID, where to find it and how to convert to entrez ID?
RNA-Seq
updated 5 days ago by
Pegasus
▴ 90 • written 3.7 years ago by
mnazir
▴ 10
3
votes
4
replies
634
views
R package DESeq2 in R 3.5.1
R
updated 26 days ago by
Ram
39k • written 5 months ago by
sehriban.buyukkilic
• 0
3
votes
6
replies
583
views
Convert Nanopore Fast5 files to Fasta format
fast5
fasta
Nanopore
14 days ago by
Sowmya Pulapet
▴ 30
3
votes
8
replies
1.3k
views
Kallisto mapping paired end
Kallisto
mapping
updated 25 days ago by
Ram
39k • written 15 months ago by
Dk
▴ 20
3
votes
6
replies
1.1k
views
how to get total read count, mapped read count and unmapped read count from multiple sam or bam files
RNAseq
PYTHON
R
bash
updated 22 days ago by
Ram
39k • written 2.7 years ago by
Bioinfonext
▴ 430
3
votes
5
replies
432
views
STAR error with a loop
STAR
RNA
transcriptomics
updated 26 days ago by
Ram
39k • written 6 months ago by
luzglongoria
▴ 40
3
votes
16
replies
9.9k
views
combining z-scores into a single z-score value
excel
R
statistics
updated 8 days ago by
Ram
39k • written 4.2 years ago by
Star
▴ 60
3
votes
3
replies
484
views
[bwa_aln_core] calculate SA coordinate... script.sh: line 91: 183402 Killed
HPC
BWA
Alignment
updated 25 days ago by
Ram
39k • written 16 months ago by
qstefano
▴ 20
3
votes
4
replies
3.8k
views
What are the Pros and Cons of working in Bioinformatics???
career
bio
updated 19 days ago by
Ram
39k • written 5.3 years ago by
scottschu97
▴ 20
3
votes
7
replies
1.6k
views
align_and_estimate_abundance error Trinty
align_and_estimate_abundance
RNA-SEQ
RSEM
Trinity
updated 23 days ago by
Ram
39k • written 20 months ago by
Princy
▴ 60
2
votes
2
replies
308
views
DESeq factor order
DESeq2
20 days ago by
Chris
▴ 10
2
votes
3
replies
863
views
Freebayes command stopped due to lack of space
freebayes
SNP-calling
updated 14 days ago by
Ram
39k • written 5.0 years ago by
amcheroo
• 0
2
votes
1
reply
203
views
P values on box plots
sequencing
Statistics
RNA
updated 27 days ago by
Basti
★ 1.6k • written 27 days ago by
Abdullah
▴ 10
2
votes
3
replies
690
views
Including bioinformatics into an agriculture/horticulture dissertation project
agrobioinformatics
plant-gene-analysis
updated 7 days ago by
Ram
39k • written 4.1 years ago by
cipri91rusu
• 0
2
votes
3
replies
381
views
Samtools faidx can't be run in succession on two reference files?
Samtools
25 days ago by
DdogBoss
• 0
600 results • Page
1 of 12
Recent Votes
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
Answer: Extract sequences from a fastq file by a list of IDs
Answer: Differences in GTF files hg19 and hg38
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Payal
▴ 140
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▴ 20
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Rory Stark
★ 1.8k
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Recent Replies
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.
Comment: Is PanCan data microarray or rna-seq
by
solarchan7
• 0
Hi, so this [paper](https://www.nature.com/articles/s41598-019-45165-4) uses the TCGA dataset and in the supplementary information, it ment…
Comment: counts matrix should be numeric, currently it has mode: character when using a c
by
Darked89
4.4k
Since the input file is named `normalized.csv` and the values look like floats most likely the counts have been already normalized somehow.
Comment: Embryo transcriptome
by
Basti
★ 1.6k
https://www.ebi.ac.uk/ena/browser/view/PRJEB11202 https://www.ebi.ac.uk/ena/browser/view/PRJNA153427
Comment: ChatGPT optimized for bioinformatics questions
by
ATpoint
72k
How is it trained on PubMed/papers? One major drawback of ChatGPT is that it wildly makes up papers that do not even exist but with great c…
Answer: sgRNA design
by
ATpoint
72k
gRNAs are single-stranded and by this they have a strand-specificity (depends where the PAM is) and that gives them an orientation.
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