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855 results • Page
1 of 18
Sort: Votes
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Views
Votes
Replies
18
votes
4
replies
8.0k
views
How To Find Rna-Seq Data Of Published Papers?
geo
next-gen
RNA-seq
updated 23 days ago by
Ram
38k • written 9.6 years ago by
user
▴ 930
14
votes
5
replies
2.7k
views
bioinformatics basic training
genome
updated 9 days ago by
Ram
38k • written 8.3 years ago by
f.muoghalu
• 0
10
votes
15
replies
5.1k
views
convert fasta/gb to vcf
fasta
vcf
genbank
gff
updated 13 hours ago by
Ram
38k • written 4.5 years ago by
marongiu.luigi
▴ 670
10
votes
6
replies
2.6k
views
which language to use for such a bioinformatics web services infrastructure?
web-services
java
updated 1 day ago by
Ram
38k • written 7.8 years ago by
lait
▴ 170
9
votes
16
replies
2.9k
views
6 follow
covert SAM to full length fasta
fasta
SAM
updated 15 hours ago by
Ram
38k • written 4.6 years ago by
marongiu.luigi
▴ 670
9
votes
20
replies
3.2k
views
Solve SAM issues flagged by Picard's ValidateSamFile
Picard
SAM
updated 15 hours ago by
Ram
38k • written 4.6 years ago by
marongiu.luigi
▴ 670
8
votes
25
replies
1.9k
views
construction of a database
sql
noSQL
neo4j
database
updated 1 day ago by
Ram
38k • written 22 months ago by
Debut
▴ 20
8
votes
12
replies
2.4k
views
Use BLAST Command Line Applications to run a folder of many sequences against a database
BLAST
updated 5 days ago by
Ram
38k • written 19 months ago by
daver.v
▴ 30
7
votes
4
replies
1.2k
views
So many Zeros (read counting)_NGS sequence analysis with R / Bioconductor: RNA-Seq workflow
alignment
RNA-Seq
R
updated 8 days ago by
Ram
38k • written 4.7 years ago by
healing80
• 0
7
votes
10
replies
1.1k
views
col as names [solved]
R
updated 5 days ago by
Ram
38k • written 4.0 years ago by
demoraesdiogo2017
▴ 90
7
votes
6
replies
1.3k
views
How to get/calculate coverage of a gene using bed file?
bed
coverage
gene
updated 14 hours ago by
Ram
38k • written 16 months ago by
Nikhil
▴ 10
7
votes
4
replies
1.7k
views
useful and freely available softwares for Bioinformatics
software
updated 5 days ago by
Ram
38k • written 8.0 years ago by
Mo
▴ 920
6
votes
12
replies
1.2k
views
VCF files 101 - for people from non Bioinformatics Background
vcf
sequencing
genome
variant-calling
updated 9 days ago by
Ram
38k • written 2.6 years ago by
akshaykum684
▴ 20
6
votes
12
replies
1.1k
views
Good tutorials/textbooks/articles to introduce biomarker discovery to a biologist?
r
biomarker
updated 5 days ago by
Ram
38k • written 4.2 years ago by
english.server
▴ 290
6
votes
6
replies
3.5k
views
Already Working In The Field Of Bioinformatics With A Bachelors, Is A Masters Degree Worth The Time?
masters
career
updated 22 days ago by
Ram
38k • written 9.5 years ago by
ashah90
▴ 30
6
votes
13
replies
606
views
Error with STAR
STAR
updated 13 days ago by
Ram
38k • written 16 days ago by
Chris
▴ 70
6
votes
11
replies
699
views
Calculate RPKM
RPKM
2 days ago by
Chris
▴ 70
6
votes
3
replies
3.1k
views
Comment On The Introduction Of A Bioinformatics Paper
publication
bayesian-model
updated 16 days ago by
Ram
38k • written 9.0 years ago by
Faheemmitha
▴ 210
6
votes
6
replies
908
views
RNA-seq pipeline for degraded RNA
RNA-Seq
degraded
pipeline
alignment
updated 17 days ago by
yussab
▴ 80 • written 2.2 years ago by
oludhe
▴ 60
6
votes
7
replies
825
views
to mark the duplicates
Assembly
updated 9 days ago by
Ram
38k • written 3.8 years ago by
manubiomed20
▴ 10
6
votes
9
replies
4.7k
views
Best Possible set of Python interview questions for Bioinformatics, that a recruiter can ask?
python
updated 2 days ago by
Ram
38k • written 7.9 years ago by
gaurav.singh
▴ 10
5
votes
6
replies
418
views
I can not allocate ram memory for WSL2
WSL2
8 days ago by
ailton
• 0
5
votes
4
replies
502
views
Converting Bam file to Fasta (Zipped)
samtools
bamtofastq
bedtools
paired
9 days ago by
Eliveri
▴ 320
5
votes
11
replies
3.0k
views
Convert Plink to Arlequin
software-error
plink
Arlequin
PGDSpider
updated 8 days ago by
Ram
38k • written 4.9 years ago by
HG
▴ 30
5
votes
6
replies
602
views
Filter out Bam not overlapping with Bed File (keeping a read and its mate)?
mates
bed
bam
samtools
9 days ago by
Eliveri
▴ 320
4
votes
3
replies
679
views
Bioinformatics courses online?
courses
updated 15 days ago by
Ram
38k • written 19 months ago by
valentinavan
▴ 50
4
votes
2
replies
902
views
Convert BAM files to GENOMEDATA files
BAM
genomedata
updated 13 hours ago by
Ram
38k • written 4.9 years ago by
Armand
• 0
4
votes
9
replies
6.7k
views
bcftools consensus command
vcf
bcftools
updated 13 hours ago by
Ram
38k • written 3.2 years ago by
Begonia_pavonina
▴ 90
4
votes
7
replies
2.0k
views
How to move the files from sub folder and sub-sub folders into one other folder?
bash
updated 17 hours ago by
Ram
38k • written 20 months ago by
mathavanbioinfo
▴ 70
4
votes
5
replies
511
views
Need help to perform survival analysis
survival
analysis
mirna
updated 10 days ago by
Mensur Dlakic
★ 23k • written 11 days ago by
Bhanu
• 0
4
votes
1
reply
308
views
Batch effect correction methods (Seurat v3, Harmony, fastMNN, Liger)
integration
Batch
seurat
fastMNN
Harmony
23 days ago by
re_raz
▴ 50
4
votes
4
replies
2.5k
views
What Statistical Test Is Appropriate When Comparing Rna-Seq Data Obtained From Biological Replicates Mapped To Different Genomes
RNA-seq
updated 27 days ago by
Ram
38k • written 10.2 years ago by
xs57
▴ 20
4
votes
8
replies
1.3k
views
6 follow
building snpEff database
snpEff
updated 29 days ago by
Ram
38k • written 10 months ago by
aabhordia
▴ 20
3
votes
8
replies
254
views
getting coding exon information from Ensembl API
Ensembl
API
updated 16 hours ago by
Ram
38k • written 21 hours ago by
Nobody
▴ 30
3
votes
2
replies
342
views
A way to find which genome builds a package supports
Bioconductor
genome
R
build
updated 11 days ago by
ATpoint
70k • written 12 days ago by
dshcherbo
• 0
3
votes
2
replies
148
views
Power analysis for patient samples
RNA-seq
1 day ago by
aropri
▴ 130
3
votes
0
replies
1.8k
views
Combined VCF file for all GTEx genotype calls?
GTExv7
GTEx
Genotype
dbGap
VCF
updated 15 hours ago by
Ram
38k • written 5.5 years ago by
django.waddle
▴ 60
3
votes
1
reply
193
views
analysing nanopore amplicon data
amplicon
genotyping
nanopore
ampliSAS
updated 21 days ago by
dthorbur
▴ 410 • written 22 days ago by
khoojj
▴ 20
3
votes
1
reply
2.1k
views
reference and effective allele
snp
updated 13 days ago by
Ram
38k • written 8.3 years ago by
alex.crimi
• 0
3
votes
6
replies
4.3k
views
Why Do I Get A Makeblastdb Error: File Does Not Match Input Format Type, Default Input Type Is Fasta
genomics
blast-plus
updated 21 days ago by
Ram
38k • written 9.3 years ago by
alok.helix
▴ 120
3
votes
2
replies
499
views
[bam-readcount v.0.8.0] Fail to open BAM file –q
bam-readcount
BAM
updated 15 hours ago by
Ram
38k • written 22 months ago by
vanessagpds
▴ 10
3
votes
3
replies
391
views
SamSort gatk invalid argument / no space left on disk
picard
gatk
samsort
nextflow
9 days ago by
Eliveri
▴ 320
3
votes
4
replies
243
views
Creating sample groups from a combination of genes for survival analysis
Survival
1 day ago by
krushnach80
★ 1.1k
3
votes
5
replies
1.7k
views
htseq counts to make matrix in Rstudio
RNA-Seq
updated 13 days ago by
Ram
38k • written 2.6 years ago by
simplysarah
• 0
3
votes
3
replies
332
views
Same pipeline produces different results
Cellranger
scRNaseq
genome
countmatrix
updated 29 days ago by
Jesse
▴ 500 • written 5 weeks ago by
Tadeoye
▴ 30
3
votes
5
replies
1.9k
views
Cellranger count command for single end fastq
RNA-Seq
sequencing
updated 22 days ago by
Ram
38k • written 2.3 years ago by
sidrah.maryam
▴ 40
3
votes
3
replies
1.1k
views
What is dbsnp file and how can I find it?
SNP
updated 9 days ago by
Ram
38k • written 2.2 years ago by
dsh.shadi
• 0
3
votes
2
replies
230
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
PAAD
KM
Plot
TCGA
17 hours ago by
Manav
• 0
3
votes
4
replies
461
views
Genome Reference Consortium Human Build - Transcriptome Size Query
GRC
updated 5 days ago by
Ram
38k • written 10 months ago by
Oligo96
• 0
3
votes
6
replies
1.7k
views
Methods and type datastructures use by Splign?
data-structure
splign
updated 1 day ago by
Ram
38k • written 6.4 years ago by
Esaie
▴ 160
855 results • Page
1 of 18
Recent Votes
Answer: Multiple samples and species with kallisto bus(tools)
Answer: Using AWS for Bioinformatics
Comment: correlations in R
Comment: Informations for gene summary are missing in eutils api of NCBI?
Confused about which comparison to give a more accurate answer in RNA seq experimen t
Basic normalization, batch correction and visualization of RNA-seq data
Answer: Stringtie does not work with NCBI GTF file?
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Comment: Weird looking dispersion & MA plot?
by
ATpoint
70k
This needs more prefiltering most likely. A filter of sum more than 100 is imo not meaningful at this sample size, it can still retain gene…
Comment: Multiple samples and species with kallisto bus(tools)
by
tritone_858
• 0
Thanks @dsull. Inevitably just after I posted, I found that cellranger can also take a custom reference constructed from multiple species, …
Answer: Clinvar Mapping
by
Pierre Lindenbaum
153k
get a BED file for your bed. get the indexed VCF for clinvar: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/ Query the VCF for …
Comment: correlations in R
by
rene.j.erhardt
• 0
That's what I thought too and I checked again. Turns out my mistake was using the default for the lo of 50 and asking for Spearman when I d…
Comment: Informations for gene summary are missing in eutils api of NCBI?
by
dare_devil
★ 1.7k
It's giving me the informations using your commands but the output is generated in txt format. How can I get the json of the same
Comment: Informations for gene summary are missing in eutils api of NCBI?
by
Mensur Dlakic
★ 23k
Maybe this command: efetch -db gene -id 85009 -mode json -format full_report I've never used this tool before, but it seems to me tha…
Comment: correlations in R
by
Mensur Dlakic
★ 23k
Established packages are unlikely to make errors in calculating a simple thing such as correlation coefficients. Chances are that something…
Comment: TSV with multi-allelic sites to VCF
by
barslmn
★ 1.3k
I have created a tutorial about converting tsv to vcf a few months earlier that might be used as a guide. https://www.biostars.org/p/955089…
Comment: How to find promoter sequence of a gene?
by
sunyeping
▴ 40
Thank you for your response. I would like to identify promoters of eukaryote genes, for example, the promoters of Itga1 and Itgae genes. Wh…
Comment: HaplotypeCaller GENOTYPE GIVEN ALLELES doesn't genotype given alleles
by
dthorbur
▴ 410
I've not used a SNP database in my analyses on non-model organisms, but I believe you are looking for the [VariantAnnotator](https://gatk.b…
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11k
> looks totally different from what I expected What did you expect? Do you have 3 replicates of untreated control, and 96 replicates of th…
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Art_SG
• 0
Yes, I sent them a ticket about it already. I will post if have any reasonable response. So far for 70% datasets that I was trying result i…
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Having looked a little more in depth into the requirements of JAFFAL, it's actually not recommended to be used with Nanopore due to the rel…
Comment: Using AWS for Bioinformatics
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Simon
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Thanks for your guidance Mensur, much appreciated
Answer: Astalavista landscape AS gtf file output
by
xizengde
• 0
Hi! I have the same problem. How do you solve the problem finally?
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