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1,000 results • Page
2 of 20
Sort: replies
Rank
Views
Votes
Replies
1
vote
12
replies
1.2k
views
Volcano plot interpretation
EnhancedVolcano
volcano-plot
updated 3 months ago by
Ram
39k • written 22 months ago by
fahim
▴ 20
7
votes
12
replies
812
views
Integrated genes from bulk RNA seq and ATAC seq
bulk-RNA
integrated
ATAC-seq
updated 3 days ago by
Sasha
▴ 180 • written 9 days ago by
Chris
▴ 100
6
votes
12
replies
1.2k
views
Good tutorials/textbooks/articles to introduce biomarker discovery to a biologist?
r
biomarker
updated 10 weeks ago by
Ram
39k • written 4.3 years ago by
english.server
▴ 290
0
votes
12
replies
1.6k
views
bedtools intersect issue
bed
bedtools
updated 9 weeks ago by
Ram
39k • written 4.7 years ago by
elisheva
▴ 120
5
votes
12
replies
627
views
Data from an experiment
single-cell
updated 3 months ago by
GenoMax
129k • written 3 months ago by
Chris
▴ 100
1
vote
12
replies
3.2k
views
How to run multiple alignment and SNP-calling of WGS data in .gb and .fasta using Python or Ruby/Java or any free software?
alignment
sequencing
software
updated 11 months ago by
Ram
39k • written 8.1 years ago by
fashiondesignrussian
▴ 60
6
votes
12
replies
1.3k
views
VCF files 101 - for people from non Bioinformatics Background
vcf
sequencing
genome
variant-calling
updated 10 weeks ago by
Ram
39k • written 2.7 years ago by
akshaykum684
▴ 20
1
vote
12
replies
3.2k
views
dN/dS analysis of genomes
genome
sequence
alignment
7 months ago by
Mehmet
▴ 800
2
votes
12
replies
632
views
how to align an intron from a complex
genomic
updated 11 months ago by
WouterDeCoster
47k • written 11 months ago by
Bioinfo
• 0
0
votes
12
replies
2.3k
views
Tax4Fun2 - error
tax4fun
silva
blast
updated 9 months ago by
GenoMax
129k • written 15 months ago by
ymj
▴ 10
1
vote
12
replies
3.3k
views
why different outputs with applying various extracting fasta sequences tool, which one correct!?
alignment
sequencing
RNA-Seq
updated 7 months ago by
Ram
39k • written 7.8 years ago by
seta
★ 1.8k
2
votes
12
replies
868
views
how to get to a VCF from bam files
Mpileup
Samtools
BAM
bcftools
VCF
updated 9 weeks ago by
Ram
39k • written 9 weeks ago by
Human
• 0
8
votes
12
replies
2.7k
views
Use BLAST Command Line Applications to run a folder of many sequences against a database
BLAST
updated 10 weeks ago by
Ram
39k • written 21 months ago by
daver.v
▴ 30
0
votes
12
replies
2.7k
views
Allpaths- Keep getting ConvertToFastbQualb.pl failed for group 'paired_ends' when I run PrepareAllPaths
next-gen
Assembly
updated 5 months ago by
Ram
39k • written 7.9 years ago by
mafireyi
▴ 80
2
votes
12
replies
4.2k
views
Adding barcodes to forward and reverse reads after sequencing
obitools
barcoding
next-gen-sequencing
updated 3 months ago by
Ram
39k • written 8.0 years ago by
cmogren
▴ 20
4
votes
12
replies
1.0k
views
Bulk RNA seq: all p adjusted are the same
p-adj
RNA-seq
differential-gene-expression
updated 5 months ago by
Ram
39k • written 12 months ago by
nils.simon.biology
▴ 10
1
vote
12
replies
3.7k
views
Can anyone explain the weird Insert Size HIstogram
RNA-Seq
alignment
sequencing
updated 4 months ago by
ATpoint
72k • written 5.7 years ago by
SMILE
▴ 170
2
votes
12
replies
1.4k
views
The best way to get gene lengths for 15K+ genes?
r
EDAseq
RNA-seq
8 months ago by
JACKY
▴ 80
0
votes
12
replies
2.9k
views
comparative analysis of two strains of bacteria's genomes
genome
gene
updated 10 days ago by
Ram
39k • written 5.6 years ago by
fonteneaudam
▴ 20
6
votes
12
replies
545
views
Help with error in cellranger
Cellranger
updated 11 days ago by
GenoMax
129k • written 12 days ago by
Chris
▴ 100
3
votes
11
replies
885
views
RepeatMasker error
repeatmasking
transciptome
RNA-seq
updated 10 months ago by
mark.ziemann
★ 1.8k • written 10 months ago by
barrypraveen
▴ 110
0
votes
11
replies
873
views
Problem with Trimmomatic Multiple Paired-End sequencing.
Trimmomatic
updated 4 months ago by
GenoMax
129k • written 4 months ago by
john
• 0
0
votes
11
replies
2.4k
views
mpiBLAST Score and E-value Calculation
blast
sequence
updated 12 months ago by
Ram
39k • written 8.2 years ago by
Lakshman Rao
• 0
1
vote
11
replies
3.0k
views
merge samples in phyloseq returns NAs
R
phyloseq
biom
updated 6 months ago by
joe.e.weaver
• 0 • written 2.9 years ago by
annaA
▴ 10
10
votes
11
replies
8.3k
views
How to adjust my manhattan plot to look better?
qqman
manhattan
R
updated 12 months ago by
Ram
39k • written 8.2 years ago by
SheelS
▴ 40
4
votes
11
replies
2.7k
views
Please add an explicit type tag :NAME
software-error
next-gen
genome
updated 3 months ago by
Ram
39k • written 5.1 years ago by
mahdikhadem95
▴ 30
4
votes
11
replies
1.1k
views
Running STAR
STAR
9 months ago by
Chris
▴ 100
0
votes
11
replies
1.5k
views
Error in Importing data in qiime2
Metagenomics
Sequencing
Qiime2
Amplicon
10 months ago by
Vaishnavi
• 0
5
votes
11
replies
6.4k
views
Error while running miso
RNA-Seq
splicing
updated 9 months ago by
Ram
39k • written 7.8 years ago by
priyankamaripuri
▴ 40
4
votes
11
replies
2.5k
views
7 follow
Getting coding sequence length
NCBI
Gene
CDS
updated 11 months ago by
newbio17
▴ 360 • written 2.9 years ago by
fi1d18
★ 4.2k
8
votes
11
replies
1.3k
views
using STAR instead of HISAT2
STAR
updated 10 months ago by
Ram
39k • written 10 months ago by
Chris
▴ 100
1
vote
11
replies
3.0k
views
bedtools fisher interpretation of "in -a" "not in -b"
fisher
bedtools
intersection
updated 3 months ago by
Ram
39k • written 5.3 years ago by
jomo018
▴ 720
0
votes
11
replies
902
views
Python - Samtools mpileup find snps with allele frequency
snp
mpileup
python
samtools
11 months ago by
pablosolar.r
▴ 20
4
votes
11
replies
6.5k
views
Correct way to calculate VAF (Variant allele fraction) from a VCF file
VCF
snp
9 months ago by
prasundutta87
▴ 650
5
votes
11
replies
3.1k
views
Convert Plink to Arlequin
software-error
plink
Arlequin
PGDSpider
updated 10 weeks ago by
Ram
39k • written 5.1 years ago by
HG
▴ 30
6
votes
11
replies
910
views
Calculate RPKM
RPKM
9 weeks ago by
Chris
▴ 100
2
votes
10
replies
6.1k
views
fq.gz file use
BioEdit
R
updated 10 weeks ago by
Ram
39k • written 4.2 years ago by
choi.yisoo.hi
• 0
5
votes
10
replies
881
views
How to change chromosome names in assembly fasta downloaded from NCBI?
grch38
ncbi
grch37
fasta
8 months ago by
magnolia
▴ 20
2
votes
10
replies
948
views
R-studio freezes error
RStudio
offtopic
updated 7 months ago by
Ram
39k • written 7 months ago by
Amr
▴ 140
2
votes
10
replies
684
views
Can I directly compare the regions defined by peaks from pair-end 50 and pair-end 100 ATAC-seq?
ATAC-seq
updated 8 months ago by
ATpoint
72k • written 8 months ago by
Dan
▴ 120
0
votes
10
replies
1.2k
views
DeSeq2 "some values in assay are negative"
RNAseq
6 months ago by
Morris_Chair
▴ 330
0
votes
10
replies
2.0k
views
WGCNA, module trait relationship
R
updated 7 months ago by
priya.bmg
▴ 60 • written 2.7 years ago by
sadeghi.reyhane
• 0
0
votes
10
replies
804
views
using txt file to pass pathways for pipelines
muscle
seqkit
bash
fasta
updated 10 months ago by
Ram
39k • written 10 months ago by
Hugo
• 0
5
votes
10
replies
4.6k
views
Antisense transcription - how to detect it?
RNA-Seq
antisense
updated 9 months ago by
Ram
39k • written 7.6 years ago by
John
13k
7
votes
10
replies
1.3k
views
Ubuntu 20.04 Crash
Ubuntu
updated 3 months ago by
Ram
39k • written 16 months ago by
bala
• 0
0
votes
10
replies
3.1k
views
6 follow
Error message running GeMoMa
gene
updated 8 months ago by
GenoMax
129k • written 3.9 years ago by
valopes
▴ 30
4
votes
10
replies
3.6k
views
TCGA normalized count data of 1000 samples for DGE
RNA-Seq
TCGA
updated 4 months ago by
Ram
39k • written 8.1 years ago by
David_emir
▴ 460
7
votes
10
replies
1.2k
views
col as names [solved]
R
updated 10 weeks ago by
Ram
39k • written 4.2 years ago by
demoraesdiogo2017
▴ 90
2
votes
10
replies
1.2k
views
multiple FASTA sequnces in to one full sequnce according to their chromosome number
NGS
FASTA
bam
updated 10 weeks ago by
Ram
39k • written 4.2 years ago by
Anu
• 0
5
votes
10
replies
405
views
Error when viewing a bam file
samtools
26 days ago by
Chris
▴ 100
1,000 results • Page
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Answer: IGV displays genomic coordinates in a 1-based system or 0-based?
RNAseq expression data log2 transformed has negative values.
Samtools: "Too Many Open Files"
Filtering bad quality probes in illumina microarray data
gene filtering for agilent microarray using Limma
A: Identification Of Significant Differences Between Phylogentic Trees Using Distan
A: How to filter vcf file on minimum genotype depth and quality for each sample
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Answer: Counting intronic reads in bulk RNA-seq
by
swbarnes2
13k
Are you sure this is appropriate for bulk RNASeq? I thought intronic reads for single cell were only counted in nuclear preps.
Answer: Single cell chemistry
by
swbarnes2
13k
Are you sure these samples are 10x? How likey is it that the sequencing group messed up and ran the samples wrongly?
Comment: How to deal with duplicated gene IDs in TCGA RNA expression data?
by
Vincent Laufer
★ 2.8k
are they distinct transcript IDs but the same gene ID? can you provide any additional context?
Comment: SyntaxError (Perhaps you forgot a comma?) in snakefile when running FastQC.
by
Dhatri Badri
• 0
that didn't work either
Answer: Why are some WES VCFs larger than others?
by
Vincent Laufer
★ 2.8k
Hi @kermit and prash (and others)! Nice discussion. I wanted to offer some **biological rationales** in addition to the technical reasons …
Answer: SyntaxError (Perhaps you forgot a comma?) in snakefile when running FastQC.
by
WouterDeCoster
47k
There is no `:` after `rule fastqc`
Comment: SyntaxError (Perhaps you forgot a comma?) in snakefile when running FastQC.
by
Dhatri Badri
• 0
sorry that was a typo while i was copying my code! I still get the same error
Comment: too many zeros in 16S rRNA amplicon sequencing data
by
andres.firrincieli
3.3k
You have too many ASV (40k) and I think this is a problem related to the denoising (DADA2) of NovaSeq 6000 sequencing data. Maybe this post…
Answer: SyntaxError (Perhaps you forgot a comma?) in snakefile when running FastQC.
by
Pierre Lindenbaum
154k
> fastq.gz". what is the dot after `fastq.gz" ` ?
Comment: DownsampleSam
by
Pierre Lindenbaum
154k
1) I think this is just a warning 2) there must be another error displayed 3) look at samtools view --subsample 4) don't use loops but use…
Comment: ABySS genome assembler
by
npavliukovec
• 0
Hello, yes, I tried it, but I have to do my home work on university's remote computer, unfortunatelly I go an error, when I try to use abys…
Comment: desgin a primer for CDS
by
yuxiang
• 0
how can you know the primer is not bind to other gene site? how can you desgin an experiment? I use the FISH to identify the gene, how abo…
Comment: desgin a primer for CDS
by
yuxiang
• 0
sorry for my late reply, I am a student, my profossor ask me to dsgin a primer for the specific cDNA, I have solved now, thanks for your re…
Comment: vg: Mapping fewer reads to a genome graph than a linear reference
by
samuel.a.odonnell
▴ 470
In this case filtering for quality might help correct for this overattributing feature?
Comment: ABySS genome assembler
by
GenoMax
129k
Did you see this guidance from ABySS manual: https://github.com/bcgsc/abyss#optimizing-the-parameters-k-and-kc
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