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832 results • Page
1 of 17
Sort: Votes
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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
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 15 hours ago by
Ram
43k • written 12.7 years ago by
Panos
★ 1.8k
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
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
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
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
75
votes
19
replies
3.3k
views
11 follow
Blog:
A list of technical advantages of Snakemake over Nextflow | Cloud solution for Snakemake
Snakemake
updated 27 days ago by
LauferVA
4.1k • written 6 months ago by
Kenny
▴ 30
70
votes
29
replies
15k
views
13 follow
Tutorial:
Generating consensus sequence from bam file
fasta
consensus
bam
updated 14 days ago by
jkbonfield
★ 1.2k • written 5.1 years ago by
finswimmer
16k
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
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 19 hours ago by
Istvan Albert
100k • written 8.1 years ago by
Ram
43k
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
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
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
34
votes
16
replies
20k
views
14 follow
Tutorial:
TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen
GDC
R
TCGA
updated 9 days ago by
aUser
▴ 30 • written 7.5 years ago by
martinguerrerog89
▴ 310
31
votes
12
replies
831
views
7 follow
Forum:
Nextflow and self-made pipelines opinion
nextflow
pipeline
data-analysis
28 days ago by
karlaarz
▴ 90
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
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
25
votes
15
replies
7.6k
views
9 follow
Randomize Read Order In Multigbp Fastq File?
fastq
updated 16 days ago by
Cliff
• 0 • written 12.8 years ago by
2184687-1231-83-
★ 5.1k
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
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
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
17
votes
8
replies
5.0k
views
Mean Variance Relationship single cell RNA-Seq Data
RNA-Seq
variance
deseq2
single cell
updated 16 days ago by
thomas.heigl.ibk
• 0 • written 3.3 years ago by
kw486
▴ 30
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
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
15
votes
9
replies
606
views
Forum:
F*up Night style events for Bioinformatics ? Comment if you're interested!
mistakes
updated 11 hours ago by
Dave Carlson
★ 1.7k • written 15 hours ago by
Ann
★ 2.4k
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
15
votes
6
replies
599
views
Need consultation about my rna-seq workflow
RNA-seq
Gene-expression
updated 7 days ago by
Ram
43k • written 9 days ago by
markusz
▴ 10
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
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
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
12
votes
14
replies
2.4k
views
8 follow
Forum:
Recovering bam files after unknown deletion in the storage
photorec
bam
sequencing
written 4.8 years ago by
Gabriel Wajnberg
▴ 70
12
votes
7
replies
6.7k
views
Forum:
Differences between SMART-seq2, SMART-seq3, and 10x
cell
smartseq
UMIs
single
10x
updated 3 days ago by
dsull
★ 5.7k • written 2.6 years ago by
hamarillo
▴ 70
12
votes
12
replies
788
views
Processing fastq files for genome assembly
fastq
vcf
assembly
amino-acid
updated 19 days ago by
Brian Bushnell
20k • written 21 days ago by
Neil
▴ 20
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
11
votes
7
replies
894
views
Shrink logFC values after edgeR
logFC
edgeR
updated 5 days ago by
Gordon Smyth
★ 6.9k • written 8 weeks ago by
arvind.1
▴ 10
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
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
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
9
votes
8
replies
5.6k
views
7 follow
CONTRA for CNV detection. troubleshooting
genome
next-gen-sequencing
cnv
software-error
updated 15 hours ago by
Ram
43k • written 9.8 years ago by
Kizuna
▴ 870
9
votes
7
replies
519
views
Getting fasta file from the VCF after variant calling
fastq
pangolin
assembly
updated 19 days ago by
Michael
54k • written 21 days ago by
Neil
▴ 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
8
votes
1
reply
242
views
News:
Registration OPEN: 8th Berlin Summer School in NGS Data Analysis (June 10-14, 2024)
Workshop
DNA-Seq
RNA-Seq
Illumina
updated 17 days ago by
JohnBlue81
▴ 500 • written 21 days ago by
David Langenberger
11k
8
votes
2
replies
560
views
News:
LAST CALL - Single-Cell RNA-Seq Data Analysis: A Practical Introduction (May 6-8, 2024 in Berlin)
single-cell
sequencing
23 days ago by
David Langenberger
11k
8
votes
12
replies
1.0k
views
7 follow
How to speed-up to contruct phylogenetic tree
MEGA
tree
phylogenetic
updated 15 days ago by
Joe
21k • written 3 months ago by
Nelo
▴ 20
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
8
votes
6
replies
405
views
Pangenome of plant
pangenome
plant
updated 1 day ago by
talbots
• 0 • written 2 days ago by
analyst
▴ 10
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
8
votes
5
replies
446
views
Overriding a color palette in R to emphasize specific data points
R
ggplot2
updated 14 days ago by
swbarnes2
14k • written 15 days ago by
jen
▴ 10
8
votes
4
replies
537
views
Why employ normalization methods, and how can they be utilized in DEG analysis?
R
DEGs
normalization
17 days ago by
wyt1995
▴ 30
832 results • Page
1 of 17
Recent Votes
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!
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
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Pierre Lindenbaum
160k
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brian.fristensky
▴ 460
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★ 2.4k
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104k
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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…
Comment: Error in openning FastQC
by
GenoMax
140k
At this point it would be beneficial to learn some of the basics of command line. Please use this UNIX tutorial since you seem to be new to…
Comment: vcf file: number of samples does not match number of columns
by
Pierre Lindenbaum
160k
> ore or have any suggestions for fixing it? it's a problem with your upstream process. You'd better fix it.
Comment: Error in openning FastQC
by
friszd
• 0
after running fastqc -o output.html input.fastq, terminal returns: " Specified output directory 'output.html' does not exist " , when i run…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
The question you should be looking into is why the Q scores are dropping there? Are there `N` calls indicating some issue with that cycle?
Comment: Error in openning FastQC
by
GenoMax
140k
What is `ctrl+c ctrl+v`? You may actually be killing the running fastqc process. If you run `fastqc` interactively (like what was shown ab…
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Dave Carlson
★ 1.7k
Ugh. I've definitely done this one before as well. And was none too happy about it.
Comment: Error in openning FastQC
by
friszd
• 0
fastqc -o output.html input.fastq ctrl+c ctrl+v
Comment: Error running local blastn in R using system2
by
GenoMax
140k
What do you see if you `cat nt_euk.nal`? Do the number of pieces mentioned in that file match with what you locally have?
Comment: Low number of both surviving reads after trimming
by
GenoMax
140k
It is your data and if you want to do that it is up to you. You may be throwing away essentially good data (you should remove the nextera s…
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