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832 results • Page
1 of 17
Sort: Views
Rank
Views
Votes
Replies
362
votes
82
replies
143k
views
35 follow
Tool:
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel
next-gen
ngs
updated 2 days ago by
jena
▴ 290 • written 11.1 years ago by
ole.tange
★ 4.4k
105
votes
15
replies
111k
views
16 follow
Convertion Of Gff3 To Gtf
gtf
gff
updated 8 days ago by
xiaoleiusc
▴ 140 • written 11.8 years ago by
GouthamAtla
12k
185
votes
44
replies
83k
views
30 follow
Drawing Chromosome Ideograms With Data
ideogram
visualization
chromosome
updated 9 days ago by
Michael
54k • written 14.0 years ago by
Yuri
★ 1.7k
164
votes
70
replies
60k
views
34 follow
How To Efficiently Parse A Huge Fastq File?
fastq
next-gen-sequencing
updated 19 hours ago by
Ram
43k • written 12.7 years ago by
Panos
★ 1.8k
66
votes
23
replies
48k
views
8 follow
extract dendrogram cluster from pheatmap
R
updated 11 days ago by
Getnet Tesfaw
• 0 • written 6.3 years ago by
1769mkc
★ 1.2k
78
votes
38
replies
32k
views
15 follow
Illumina Instrument Type from fastq?
fastq
updated 28 days ago by
nickp60
▴ 60 • written 7.8 years ago by
andrew.j.skelton73
6.5k
103
votes
42
replies
30k
views
34 follow
Forum:
List of cloud genomics companies
cloud-genomics
updated 20 days ago by
Jeremy Leipzig
22k • written 10.4 years ago by
14134125465346445
★ 3.6k
41
votes
13
replies
26k
views
13 follow
Gene Set Enrichment Analysis after DESeq2
RNA-Seq
DESeq2
geneontology
GSEA
updated 21 days ago by
CTLong
▴ 90 • written 6.4 years ago by
Sreeraj Thamban
▴ 290
26
votes
5
replies
23k
views
BLAST options: max_target_seqs and num_alignments
blast
updated 7 days ago by
Lada
▴ 30 • written 9.4 years ago by
biolab
★ 1.4k
34
votes
16
replies
20k
views
14 follow
Tutorial:
TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen
GDC
R
TCGA
updated 10 days ago by
aUser
▴ 30 • written 7.5 years ago by
martinguerrerog89
▴ 310
5
votes
7
replies
19k
views
6 follow
VCF To FASTA
next-gen
genetic
genome
updated 19 days ago by
seta
★ 1.9k • written 5.2 years ago by
Myo Naung
▴ 10
21
votes
6
replies
16k
views
survfit(Surv()) P-value interpretation for 3 survival curves?
survfit
Surv
survival curves
R
updated 5 days ago by
marshelma
• 0 • written 4.5 years ago by
JJDollar
▴ 130
47
votes
15
replies
16k
views
10 follow
DESeq2 compare all levels
differential-gene-expression
RNA-Seq
DESeq2
updated 9 days ago by
Bionaught
• 0 • written 5.7 years ago by
firestar
★ 1.6k
15
votes
34
replies
16k
views
10 follow
Issues installing bcl2fastq?
bcl2fastq
demultiplexing
updated 22 days ago by
barslmn
★ 2.1k • written 6.6 years ago by
a.rex
▴ 350
70
votes
29
replies
15k
views
13 follow
Tutorial:
Generating consensus sequence from bam file
fasta
consensus
bam
updated 15 days ago by
jkbonfield
★ 1.2k • written 5.1 years ago by
finswimmer
16k
46
votes
13
replies
14k
views
13 follow
Tutorial:
Methylation Analysis Tutorial in R - Part 1
R
cancer
methylation
updated 17 days ago by
Konstantinos
• 0 • written 3.5 years ago by
Hamid Ghaedi
3.2k
12
votes
19
replies
14k
views
11 follow
SnpMatrix from VCF file
VCF
Eqtl
MatrixEQTL
SnpMatrix
vcftools
updated 14 days ago by
pmiller
▴ 10 • written 7.0 years ago by
Dhana
▴ 110
8
votes
12
replies
13k
views
11 follow
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
featureCounts
updated 26 days ago by
BioinfGuru
★ 1.6k • written 4.0 years ago by
chatterjee.arumoy
▴ 50
16
votes
7
replies
12k
views
8 follow
MAF vs VAF
sequencing
updated 4 days ago by
Ömer An
▴ 260 • written 6.0 years ago by
lauren.wahyudi
▴ 50
0
votes
3
replies
12k
views
Converting PDBQT output to PDB in VINA
Docking
PDBQT
VINA
updated 21 days ago by
Ricard
• 0 • written 8.3 years ago by
marawanhussain
▴ 30
31
votes
14
replies
12k
views
11 follow
Finding Rrna Genes In Metagenomic Data
rna
rRNA
metagenomics
updated 3 days ago by
Ram
43k • written 13.5 years ago by
toshnam
▴ 650
14
votes
9
replies
11k
views
8 follow
Downsample BAM file to specific amount of reads
bam
updated 13 days ago by
GenoMax
140k • written 2.6 years ago by
kstangline
▴ 80
49
votes
30
replies
11k
views
13 follow
Tutorial:
How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation
meta
how-to
updated 23 hours ago by
Istvan Albert
100k • written 8.1 years ago by
Ram
43k
16
votes
10
replies
10k
views
8 follow
GRCh37.p13 download at NCBI FTP?
ncbi
reference
grch37
updated 19 days ago by
Sruthi
• 0 • written 5.5 years ago by
Marvin
▴ 220
21
votes
26
replies
9.4k
views
11 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 14 days ago by
Yao
▴ 30 • written 4.3 years ago by
Juke34
8.5k
82
votes
46
replies
8.3k
views
15 follow
Tool:
ChatGPT optimized for bioinformatics questions
gpt
updated 15 days ago by
LauferVA
4.1k • written 9 months ago by
Sasha
▴ 830
25
votes
15
replies
7.6k
views
9 follow
Randomize Read Order In Multigbp Fastq File?
fastq
updated 17 days ago by
Cliff
• 0 • written 12.8 years ago by
2184687-1231-83-
★ 5.1k
15
votes
10
replies
7.5k
views
6 follow
Intersect multiple BED files
bed
intersect
updated 1 day ago by
Alex Reynolds
35k • written 8.2 years ago by
int11ap1
▴ 470
8
votes
7
replies
6.8k
views
Parse the Xml response from Entrez Db=bioproject Using Biopython eFetch
entrez
efetch
biopython
xml
updated 8 days ago by
LauferVA
4.1k • written 8.8 years ago by
Prasad
▴ 50
12
votes
7
replies
6.7k
views
Forum:
Differences between SMART-seq2, SMART-seq3, and 10x
cell
smartseq
UMIs
single
10x
updated 4 days ago by
dsull
★ 5.7k • written 2.6 years ago by
hamarillo
▴ 70
3
votes
8
replies
6.2k
views
6 follow
Download CAZy database
genome
gene
database
cazy
updated 13 days ago by
GenoMax
140k • written 6.1 years ago by
anu014
▴ 190
9
votes
8
replies
5.6k
views
7 follow
CONTRA for CNV detection. troubleshooting
genome
next-gen-sequencing
cnv
software-error
updated 19 hours ago by
Ram
43k • written 9.8 years ago by
Kizuna
▴ 870
6
votes
12
replies
5.5k
views
6 follow
Getting sample information from GEO
GEO
NCBI
updated 2 days ago by
Tania
• 0 • written 6.9 years ago by
Tom_L
▴ 350
7
votes
15
replies
5.5k
views
9 follow
convert VCF to gVCF
gVCF
VCF
updated 21 days ago by
jena
▴ 290 • written 4.5 years ago by
mateid
• 0
5
votes
5
replies
5.4k
views
beagle 4 exception: Duplicate marker
vcf
IBD
plink
beagle
updated 2 days ago by
Ram
43k • written 9.3 years ago by
galbarel
▴ 10
8
votes
16
replies
5.2k
views
9 follow
visualize CNV data based on WGS
CNV
updated 8 days ago by
clealk
▴ 50 • written 6.2 years ago by
Bogdan
★ 1.4k
12
votes
19
replies
5.2k
views
how to identify CDR region in antibody sequence
CDR
antibody
updated 28 days ago by
tiancheng
• 0 • written 21 months ago by
reany
▴ 50
18
votes
10
replies
5.2k
views
Should I normalize read counts if I want to run plotPCA?
RNA-Seq
updated 20 days ago by
ella
• 0 • written 3.9 years ago by
c_u
▴ 520
11
votes
8
replies
5.0k
views
Multi-mapping High with featureCounts but not STAR
RNA-Seq
sequencing
alignment
updated 8 days ago by
GenoMax
140k • written 4.8 years ago by
garbuzov
▴ 70
17
votes
8
replies
5.0k
views
Mean Variance Relationship single cell RNA-Seq Data
RNA-Seq
variance
deseq2
single cell
updated 17 days ago by
thomas.heigl.ibk
• 0 • written 3.3 years ago by
kw486
▴ 30
5
votes
15
replies
4.8k
views
6 follow
Why are there many reads with green color in IGV of RNA-seq data?
rna-seq
IGV
mapping
updated 6 days ago by
vague-barracuda-4686
• 0 • written 4.7 years ago by
Apprentice
▴ 160
4
votes
14
replies
4.5k
views
8 follow
Installation: Tax4Fun2 package are not found and github repository is not maintained anymore
Tax4Fun2
updated 1 day ago by
Ram
43k • written 21 months ago by
Elsa
▴ 20
9
votes
1
reply
4.4k
views
How To Generate Synthetic Read Data From An Existing Fasta
fasta
sequence
reads
updated 23 days ago by
Ram
43k • written 10.2 years ago by
smith.tracymae
• 0
9
votes
6
replies
4.4k
views
6 follow
Remove contigs that are lower than 200
assembly
sequencing
genome
next-gen
updated 20 days ago by
GenoMax
140k • written 4.1 years ago by
Bioinfo
▴ 20
2
votes
2
replies
4.3k
views
Variant calling for sanger reads
variant-calling
sanger
alignment
variants
updated 2 days ago by
Ram
43k • written 7.6 years ago by
Amirosein
▴ 70
3
votes
12
replies
4.2k
views
samtools mpileup keeps making an empty file
samtools
pileup
updated 28 days ago by
gabt
▴ 120 • written 5.2 years ago by
James Reeve
▴ 130
10
votes
6
replies
4.0k
views
Tutorial:
CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation
corlevelplot
updated 2 days ago by
Ram
43k • written 6.1 years ago by
Kevin Blighe
87k
4
votes
14
replies
4.0k
views
Trouble with bedtools getfasta
bedtools
getfasta
written 2.1 years ago by
gkunz
▴ 30
5
votes
9
replies
3.7k
views
Can one plot % of variance using the plotMDS function?
limma
plotMDS
PCA
PCoA
% of varience
updated 27 days ago by
Gordon Smyth
★ 6.9k • written 3.8 years ago by
harelarik
▴ 90
2
votes
4
replies
3.6k
views
Tutorial for analysing gpr files of microarray
GPR
microarray
updated 7 days ago by
bioyas
▴ 10 • written 5.4 years ago by
afli
▴ 190
832 results • Page
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Announcement: Research Topic "Mechanistic, Machine Learning and Hybrid Models of the 'Other' Endocrine Regulatory Systems in Health and Disease", Volume II
Comment: Number of CPUs to use by DRAP for transcriptomic assmbly
Comment: Gene reads all zero for each sample
Synthetic lethality and cancer database
Answer: log2(TPM+1)
Comment: Error in openning FastQC
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
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Comment: Mapping ortholog human and mouse transcript
by
1769mkc
★ 1.2k
for hgnc and ensembl that can be done for transcript id for human to mouse ortholog its difficult to parse and map the exact version from g…
Comment: Announcement: Research Topic "Mechanistic, Machine Learning and Hybrid Models of
by
Mensur Dlakic
★ 26k
Take it from someone who has hosted both a successful and a failed research topic: these deadlines are unrealistic. I am guessing you are p…
Answer: Tissue specific mRNA expression dataset in human and mouse
by
BioinfGuru
★ 1.6k
Awesome, years ago I wrote my thesis on the use of Tau to calculate tissue specificity, enjoy! The supplementary materials in the paper is…
Answer: Mapping ortholog human and mouse transcript
by
BioinfGuru
★ 1.6k
That error is on the server side, nothing to do with you, and is very common. Usually the fix is to try again in an hour, or to insert host…
Comment: Nanopore multisample variant calling
by
emilydolivo97
• 0
hello @colindaven , Did you find a suitable tool for this purpose please ? I'm dealing with fungal dataset
Comment: How do I get the gene annotations as a text file from a genebank file?
by
BioinfGuru
★ 1.6k
Can you upload or post a link to the genbank file please?
Comment: Mapping ortholog human and mouse transcript
by
manaswwm
▴ 490
I usually perform biomaRt queries with their `getBM()` function where I list the input using `filter` and `values` option and my request in…
Comment: DESeq2 and normalization
by
JH
• 0
Thank you for your response. I have often seen commands like dds <- estimateSizeFactors(dds) normalized_counts <- counts(dds, normalized=T…
Comment: Number of CPUs to use by DRAP for transcriptomic assmbly
by
Mohamed Abderrahmane
▴ 10
It's the case that there's no indication of multi-threading in the documentation. However, it made me wonder why the developers would restr…
Answer: Is RNAseq data from a monoclonal cell line technically considered scRNAseq?
by
Soheil
▴ 90
Bulk RNAseq from any sample is still considered a bulk sample. Running bulk RNA sequencing on a sample with any level of cell type/state c…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Yikes. Well, this is from an Illumina MiniSeq. Sure, I will use alignment, but only to remove host reads. Then the remaining reads will go …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
This is going to be tough to diagnose. Are you going to align to a reference? If so go ahead with the alignments to see if alignments turn …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Thank you for replying. I have separated the reads with at least one N on them and they account for 0.2% of the total reads in the file (8'…
Comment: Error running local blastn in R using system2
by
Mensur Dlakic
★ 26k
The `-db data/nt_euk` switch means that in your current directory you have a subdirectory called `data`, and all the `nt_euk` files are in …
Comment: Low number of both surviving reads after trimming
by
Jay
• 0
Thank you for your opinion. I will try with lower LEADING and TRAILING bases. By the way, I tried to set `keepBothReads:true` through sear…
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