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1,000 results • Page
1 of 20
Sort: Votes
Rank
Views
Votes
Replies
41
votes
55
replies
10k
views
6 follow
hash function for DNA sequences
hash
hashing
DNA
7.1 years ago by
midox
▴ 290
27
votes
17
replies
17k
views
12 follow
Dotplot for filtered pathways result
pathways
ggplot2
clusterProfiler
r
dotplot
17 months ago by
Leite
★ 1.2k
24
votes
25
replies
6.1k
views
How to generate Beta diversity boxplot from phyloseq object?
phyloseq
beta diversity
metagenomics
2.8 years ago by
dpc
▴ 240
23
votes
22
replies
40k
views
6 follow
Converting VCF to PLINK .bed binary fileset to check for pedigree errors with KING: How do conversion tools make the PLINK .fam file, without asking …
plink
vcf
fam
gatk
vcftools
updated 5 months ago by
Nicole
• 0 • written 5.1 years ago by
gaelgarcia
▴ 250
23
votes
10
replies
5.1k
views
How to predict individual ethnicity information by using hapmap data
SNP
Ethnicity
Hapmap
updated 2.1 years ago by
Kevin Blighe
85k • written 5.2 years ago by
Joe
▴ 40
22
votes
20
replies
2.1k
views
what is the prefered strategy to treat with blast-less transcriptomes from RNA-seq
blast
RNA-Seq
genome
gene
updated 7 weeks ago by
Ram
39k • written 6.9 years ago by
Farbod
★ 3.4k
22
votes
19
replies
2.5k
views
targets of a list of miRNAs
miRNAs
RNA-Seq
DEanalysis
target-prediction
6.6 years ago by
fi1d18
★ 4.2k
20
votes
17
replies
5.1k
views
HiSeq 4000 PhiX screening and removal using bbduk
spikein
filtering
bbmap
bbduk
phix
5.8 years ago by
Anand Rao
▴ 560
20
votes
15
replies
26k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink
SNP
updated 9 months ago by
Ram
39k • written 7.4 years ago by
dam4l
▴ 190
19
votes
43
replies
4.2k
views
Annotation of huge number of CNV files
CNV annotation TCGA
4.8 years ago by
nazaninhoseinkhan
▴ 510
18
votes
4
replies
8.2k
views
How To Find Rna-Seq Data Of Published Papers?
geo
next-gen
RNA-seq
updated 12 weeks ago by
Ram
39k • written 9.8 years ago by
user
▴ 930
18
votes
19
replies
1.7k
views
6 follow
Extremely important marker gene has many reads based on IGV viewer but no quantified reads
rna-seq
sequencing
igv
alignment
next-gen
updated 5 months ago by
Ram
39k • written 4.4 years ago by
rbkh09
• 0
18
votes
7
replies
899
views
How to calculate if statistically a variable of a bulk RNA-seq affects the comparison of interest?
DESeq2
Variable
RNA-seq
8 months ago by
Rafael Soler
★ 1.2k
17
votes
19
replies
2.2k
views
Sorting sequences according header
software error
sequence
Assembly
next-gen
6.7 years ago by
Gian77
▴ 60
17
votes
37
replies
3.5k
views
No alias or index file found for protein database
next-gen
software error
sequence
updated 4.0 years ago by
Biostar
20 • written 4.1 years ago by
williamsbrian5064
▴ 470
17
votes
8
replies
1.9k
views
Number of unique authors in PubMed in last 10 years
PubMed
7.2 years ago by
nejc
▴ 50
17
votes
13
replies
5.6k
views
7 follow
BWA: Why paired reads mapped to different chromosome?
alignment
genome
sequencing
6.0 years ago by
lghust2011
▴ 100
16
votes
18
replies
4.1k
views
8 follow
Python Program to read .fasta file to .txt file
Python
updated 3.8 years ago by
Mensur Dlakic
★ 23k • written 3.8 years ago by
tikshyadav19
• 0
16
votes
21
replies
1.6k
views
Why there are different hit for a same gene in different species
gene
blast
ortholog
paralog
6.6 years ago by
Farbod
★ 3.4k
16
votes
8
replies
1.7k
views
8 follow
What are the most important unresolved problems in Bioinformatics?
bioinformatics
updated 6 weeks ago by
Ram
39k • written 6.6 years ago by
chen
★ 2.4k
16
votes
14
replies
14k
views
Which truseq trimmomatic adapters file to use when removing truseq adapters?
adapters
trimmomatic
RNA-seq
4.9 years ago by
salamandra
▴ 540
16
votes
10
replies
4.8k
views
6 follow
Powerful desktop computer for genomics
next-gen
sequencing
ChIP-Seq
RNA-Seq
7.0 years ago by
Alternative
▴ 270
16
votes
16
replies
2.5k
views
Using DESeq2 results for building a classifier
deseq2
RNA-Seq
differentially expressed genes
5.2 years ago by
bioinfo456
▴ 150
16
votes
38
replies
16k
views
Differential gene Analysis by Limma
Limma
Microarray
R
updated 13 months ago by
Ram
39k • written 8.3 years ago by
Mo
▴ 920
16
votes
17
replies
2.7k
views
6 follow
RNA seq pipeline
RNA-Seq
5.6 years ago by
dimitrischat
▴ 180
15
votes
14
replies
2.4k
views
Penalty model of BWA MEM and BOWTIE2?
RNA-Seq
bwa mem
bowtie2
alignment
5.4 years ago by
John
▴ 270
15
votes
14
replies
1.5k
views
how can interpret these biologically weird results?
RNA-Seq
updated 2.3 years ago by
Biostar
20 • written 5.6 years ago by
Mozart
▴ 330
15
votes
19
replies
1.4k
views
trimmomaric command for a fasta file?
trimmomatic
updated 5.1 years ago by
Ram
39k • written 5.1 years ago by
Nadin.asal
• 0
14
votes
8
replies
4.6k
views
Unable To Replicate Splice Junction In Tophat
tophat2
bam
9.6 years ago by
Dan D
7.4k
14
votes
30
replies
2.6k
views
Download GTF/GFF annotation data for NT database, not by organism (for STAR alignment)
RNA-Seq
rna-seq
alignment
next-gen
4.1 years ago by
Malka
▴ 70
14
votes
18
replies
4.2k
views
GATK Haplotype Caller
next-gen
GATK
haplotype
caller
contigs
updated 6.4 years ago by
Biostar
20 • written 6.6 years ago by
plink_9857
▴ 50
14
votes
5
replies
2.8k
views
bioinformatics basic training
genome
updated 10 weeks ago by
Ram
39k • written 8.5 years ago by
f.muoghalu
• 0
14
votes
16
replies
1.4k
views
Why are some mapped reads not mapped completely?
RNA-Seq
mapping
updated 2.5 years ago by
lieven.sterck
14k • written 2.5 years ago by
utsafar
▴ 80
13
votes
7
replies
5.8k
views
Why some probes have "NA" for gene symbol and Entrez ID?
affymetrix microarray
NA
genesymbol
updated 6.5 years ago by
Biostar
20 • written 6.5 years ago by
Raheleh
▴ 250
13
votes
19
replies
4.4k
views
bbmerge not joining paired-end reads
bbmerge
alignment
5.5 years ago by
bioplanet
▴ 60
13
votes
13
replies
1.1k
views
Is reproducibility of identified variants in a gene important in Sanger sequencing?
reproducibility
sanger sequencing
variants
3.6 years ago by
DanielC
▴ 160
13
votes
6
replies
10k
views
6 follow
MAF vs VAF
sequencing
5.2 years ago by
lauren.wahyudi
▴ 40
13
votes
22
replies
9.2k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva
combat
batch effects
updated 5.7 years ago by
Biostar
20 • written 5.9 years ago by
lessismore
★ 1.3k
13
votes
16
replies
5.7k
views
6 follow
Confused about how to generate a consensus sequence after bwa
bwa
samtools
mpileup
4.4 years ago by
DNAngel
▴ 240
13
votes
13
replies
8.0k
views
How to do pca plot from .eigenval and .eigenvec files from Plink in R.
R
SNP
updated 5.2 years ago by
Devon Ryan
103k • written 5.2 years ago by
amitgourav.ghosh12
▴ 70
13
votes
24
replies
3.5k
views
Error of bam-to-sam conversion using samtools
samtools
TopHat2
RNA-Seq
BAM
SAM
updated 6.2 years ago by
GenoMax
129k • written 6.2 years ago by
Gary
▴ 480
13
votes
16
replies
5.1k
views
Mask or trim primer sequences in Amplicon sequencing
amplicon
mask
trimming
fastq
6.4 years ago by
Paul
★ 1.5k
12
votes
28
replies
1.9k
views
Calculating the expression level of genes
Gene expression
RNA-Seq
R
5.0 years ago by
Za
▴ 140
12
votes
10
replies
2.4k
views
7 follow
SAM / BAM alignments
SAM
BAM
6.4 years ago by
John
13k
12
votes
13
replies
2.2k
views
Gene Expression and Systems Biology (homework)
gene
homework
updated 5 months ago by
Ram
39k • written 7.9 years ago by
sarathkurichiyil
• 0
12
votes
12
replies
4.5k
views
Need A Script That Finds Whether A String In One Column Matches In Other Columns Of The Same Row
perl
updated 9.5 years ago by
Istvan Albert
98k • written 9.5 years ago by
biolab
★ 1.4k
12
votes
11
replies
2.8k
views
How To Get Snp Genotypes
snp
genotyping
updated 11.7 years ago by
Lars Juhl Jensen
11k • written 12.1 years ago by
Pri
▴ 20
12
votes
8
replies
2.7k
views
How to change depth of sequence in RNA-seq fastq files
depth of sequence
RNA-Seq
6.3 years ago by
statfa
▴ 720
12
votes
10
replies
3.7k
views
Speed up BLASTp vs NCBI nr database
blast
7.0 years ago by
biotech
▴ 570
12
votes
14
replies
4.6k
views
bedtools intersect error?
ChIP-Seq
bedtools
intersect
4.3 years ago by
star
▴ 340
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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Recent Replies
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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