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1,000 results • Page
1 of 20
Sort: Votes
Rank
Views
Votes
Replies
41
votes
55
replies
8.8k
views
6 follow
hash function for DNA sequences
hash
hashing
DNA
6.2 years ago by
midox
▴ 290
27
votes
17
replies
13k
views
12 follow
Dotplot for filtered pathways result
pathways
ggplot2
clusterProfiler
r
dotplot
6 months ago by
Leite
★ 1.2k
24
votes
25
replies
4.2k
views
How to generate Beta diversity boxplot from phyloseq object?
phyloseq
beta diversity
metagenomics
23 months ago by
dpc
▴ 240
23
votes
21
replies
30k
views
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
4.1 years ago by
gaelgarcia
▴ 250
23
votes
10
replies
4.6k
views
How to predict individual ethnicity information by using hapmap data
SNP
Ethnicity
Hapmap
updated 14 months ago by
Kevin Blighe
81k • written 4.3 years ago by
Joe
▴ 40
22
votes
19
replies
2.1k
views
targets of a list of miRNAs
miRNAs
RNA-Seq
DEanalysis
target-prediction
5.7 years ago by
Angel
★ 4.1k
22
votes
20
replies
1.8k
views
what is the prefered strategy to treat with blast-less transcriptomes from RNA-seq
RNA-Seq
blast
gene
genome
Forum
5.9 years ago by
Farbod
★ 3.3k
19
votes
43
replies
3.5k
views
Annotation of huge number of CNV files
CNV annotation TCGA
3.9 years ago by
nazaninhoseinkhan
▴ 430
18
votes
4
replies
7.6k
views
How To Find Rna-Seq Data Of Published Papers?
bioinformatics
next-gen
rna-seq
geo
8.9 years ago by
user
▴ 870
18
votes
19
replies
1.3k
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
3.5 years ago by
rbkh09
• 0
17
votes
13
replies
4.7k
views
7 follow
BWA: Why paired reads mapped to different chromosome?
alignment
genome
sequencing
5.1 years ago by
lghust2011
▴ 100
17
votes
8
replies
1.6k
views
Number of unique authors in PubMed in last 10 years
PubMed
6.3 years ago by
nejc
▴ 50
17
votes
19
replies
1.8k
views
Sorting sequences according header
software error
sequence
Assembly
next-gen
5.8 years ago by
Gian77
▴ 60
17
votes
37
replies
2.6k
views
No alias or index file found for protein database
next-gen
software error
sequence
updated 3.1 years ago by
Biostar
20 • written 3.2 years ago by
williamsbrian5064
▴ 430
16
votes
21
replies
1.3k
views
Why there are different hit for a same gene in different species
gene
blast
ortholog
paralog
5.7 years ago by
Farbod
★ 3.3k
16
votes
14
replies
12k
views
Which truseq trimmomatic adapters file to use when removing truseq adapters?
adapters
trimmomatic
RNA-seq
4.0 years ago by
salamandra
▴ 460
16
votes
18
replies
2.5k
views
8 follow
Python Program to read .fasta file to .txt file
Python
updated 2.8 years ago by
Mensur Dlakic
★ 19k • written 2.8 years ago by
tikshyadav19
• 0
16
votes
10
replies
4.3k
views
6 follow
Powerful desktop computer for genomics
next-gen
sequencing
ChIP-Seq
RNA-Seq
6.1 years ago by
Alternative
▴ 270
16
votes
38
replies
15k
views
Differential gene Analysis by Limma
Limma
Microarray
R
updated 8 weeks ago by
Ram
36k • written 7.4 years ago by
Mo
▴ 920
16
votes
8
replies
1.4k
views
8 follow
What are the most important unresolved problems in Bioinformatics?
problem
unresolved
bioinformatics
updated 5.7 years ago by
Biostar
20 • written 5.7 years ago by
chen
★ 2.4k
16
votes
17
replies
2.4k
views
6 follow
RNA seq pipeline
RNA-Seq
4.6 years ago by
dimitrischat
▴ 180
16
votes
16
replies
2.0k
views
Using DESeq2 results for building a classifier
deseq2
RNA-Seq
differentially expressed genes
4.2 years ago by
Uday Rangaswamy
▴ 150
15
votes
14
replies
1.8k
views
Penalty model of BWA MEM and BOWTIE2?
RNA-Seq
bwa mem
bowtie2
alignment
4.4 years ago by
John
▴ 240
15
votes
14
replies
22k
views
6 follow
Converting SNP from chr:pos to rs number using PLINK?
SNP
plink
updated 6.3 years ago by
Biostar
20 • written 6.5 years ago by
dam4l
▴ 180
15
votes
14
replies
1.2k
views
how can interpret these biologically weird results?
RNA-Seq
updated 17 months ago by
Biostar
20 • written 4.6 years ago by
Mozart
▴ 320
15
votes
19
replies
1.1k
views
trimmomaric command for a fasta file?
trimmomatic
updated 4.2 years ago by
Ram
36k • written 4.2 years ago by
Nadin.asal
• 0
14
votes
17
replies
4.3k
views
HiSeq 4000 PhiX screening and removal using bbduk
spikein
filtering
bbmap
bbduk
phix
4.9 years ago by
Anand Rao
▴ 510
14
votes
8
replies
4.3k
views
Unable To Replicate Splice Junction In Tophat
tophat2
bam
8.7 years ago by
Dan D
7.3k
14
votes
16
replies
959
views
Why are some mapped reads not mapped completely?
RNA-Seq
mapping
updated 19 months ago by
lieven.sterck
14k • written 19 months ago by
utsafar
▴ 80
14
votes
5
replies
2.5k
views
bioinformatics basic training
genome
Tutorial
updated 3 months ago by
Ram
36k • written 7.6 years ago by
f.muoghalu
• 0
14
votes
30
replies
2.0k
views
Download GTF/GFF annotation data for NT database, not by organism (for STAR alignment)
RNA-Seq
rna-seq
alignment
next-gen
3.1 years ago by
Malka
▴ 70
14
votes
18
replies
3.8k
views
GATK Haplotype Caller
next-gen
GATK
haplotype
caller
contigs
updated 5.5 years ago by
Biostar
20 • written 5.6 years ago by
plink_9857
▴ 50
13
votes
7
replies
5.2k
views
Why some probes have "NA" for gene symbol and Entrez ID?
affymetrix microarray
NA
genesymbol
updated 5.5 years ago by
Biostar
20 • written 5.6 years ago by
Raheleh
▴ 220
13
votes
19
replies
3.6k
views
bbmerge not joining paired-end reads
bbmerge
alignment
4.6 years ago by
bioplanet
▴ 60
13
votes
24
replies
2.7k
views
Error of bam-to-sam conversion using samtools
samtools
TopHat2
RNA-Seq
BAM
SAM
updated 5.3 years ago by
GenoMax
117k • written 5.3 years ago by
Gary
▴ 480
13
votes
16
replies
4.4k
views
Mask or trim primer sequences in Amplicon sequencing
amplicon
mask
trimming
fastq
5.5 years ago by
Paul
★ 1.4k
13
votes
13
replies
765
views
Is reproducibility of identified variants in a gene important in Sanger sequencing?
reproducibility
sanger sequencing
variants
2.7 years ago by
DanielC
▴ 150
13
votes
22
replies
8.0k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva
combat
batch effects
updated 4.8 years ago by
Biostar
20 • written 5.0 years ago by
lessismore
★ 1.2k
13
votes
13
replies
7.1k
views
How to do pca plot from .eigenval and .eigenvec files from Plink in R.
R
SNP
updated 4.3 years ago by
Devon Ryan
102k • written 4.3 years ago by
amitgourav.ghosh12
▴ 70
13
votes
16
replies
4.5k
views
6 follow
Confused about how to generate a consensus sequence after bwa
bwa
samtools
mpileup
3.5 years ago by
DNAngel
▴ 210
13
votes
6
replies
8.5k
views
6 follow
MAF vs VAF
sequencing
4.3 years ago by
lauren.wahyudi
▴ 40
12
votes
10
replies
2.0k
views
7 follow
SAM / BAM alignments
SAM
BAM
5.5 years ago by
John
13k
12
votes
13
replies
2.0k
views
Gene Expression and Systems Biology (homework)
gene
homework
7.0 years ago by
sarathkurichiyil
• 0
12
votes
14
replies
3.3k
views
bedtools intersect error?
ChIP-Seq
bedtools
intersect
3.3 years ago by
star
▴ 290
12
votes
11
replies
2.5k
views
How To Get Snp Genotypes
snp
genotyping
updated 10.8 years ago by
Lars Juhl Jensen
11k • written 11.2 years ago by
Pri
▴ 20
12
votes
28
replies
1.5k
views
Calculating the expression level of genes
Gene expression
RNA-Seq
R
4.0 years ago by
Za
▴ 140
12
votes
17
replies
3.4k
views
How do I generate all possible Newick Tree permutations for a set of species given an outgroup in Python?
Python
Newick
phylogenetics
tree
phylogeny
4.7 years ago by
anonymous1192976466
▴ 50
12
votes
12
replies
4.2k
views
Need A Script That Finds Whether A String In One Column Matches In Other Columns Of The Same Row
perl
updated 8.6 years ago by
Istvan Albert
93k • written 8.6 years ago by
biolab
★ 1.4k
12
votes
8
replies
2.3k
views
How to change depth of sequence in RNA-seq fastq files
depth of sequence
RNA-Seq
5.4 years ago by
statfa
▴ 660
12
votes
10
replies
3.3k
views
Speed up BLASTp vs NCBI nr database
blast
6.1 years ago by
biotech
▴ 540
1,000 results • Page
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Comment: Computing allele frequencies per individual for a set of SNPs in PLINK
by
chrchang523
9.3k
If 1kgtot.bim contains doubled IDs (e.g. "HG00096 HG00096", you need to provide a doubled ID to `--indv`. The log file shows that your scr…
Answer: ESTIMATE tumor purity
by
JACKY
▴ 10
Just in case anyone faces this problem in the future, here is the link for the updated `estimate package` on github: https://github.com/…
Answer: Exctract unmapped reads from BLAST
by
GenoMax
117k
> Is there a way to tell blast to output the unmapped reads into a > separate file? No there is not. You will need to use `-outfmt 7` whe…
Comment: Resfams Database usage
by
Neel
▴ 10
Hi, i have annotated genome by prokka and o want to search amr agaisnt resfams could you please tell me how to do it steps by steps.
Comment: Exctract unmapped reads from BLAST
by
Pierre Lindenbaum
146k
those are two distinct commands https://linux.die.net/man/1/comm and https://linux.die.net/man/1/join extract the names of your queries, s…
Comment: Exctract unmapped reads from BLAST
by
Pilar
• 0
Thanks for answering :), sorry, I'm new at this. These are commands I should use when I launch Blast in terminal?
Comment: Exctract unmapped reads from BLAST
by
Pierre Lindenbaum
146k
have a look at `comm` or `join`.
Comment: Computing allele frequencies per individual for a set of SNPs in PLINK
by
pifferdavide
▴ 100
Sorry I forgot to mention I used it in this loop, which worked with another plink file, but not with this 1KG file. for popfile in $(l…
Comment: Computing allele frequencies per individual for a set of SNPs in PLINK
by
chrchang523
9.3k
`--indv` takes a single ID, not a filename. So `--indv IDlist.txt` shouldn't work.
Answer: Quast Ouput
by
Ying
• 0
The "# contigs 47484" is based on contig of size >= 500 bp (see the first line of your screenshot). The "# contigs (>= 0 bp)" is the raw nu…
Answer: SRA obtained metagenomic reads appears to corrupt - cannot work on SingleM
by
Mensur Dlakic
★ 19k
Not sure why: 1) you are splitting reads; 2) you are fixing reads when they seem fine. I suggest something like this instead after `prefetc…
Comment: Quick way to get a field such as QNAME from the last read in a bam file?
by
kalavattam
▴ 70
Thank you. Do you know of any strategies for non-coordinated-sorted bam files?
Comment: analyzing a single cell and searching for a specific gene using single cell data
by
jared.andrews07
★ 13k
@rpolicastro gave you several helpful links for using the h5ad file, in addition to how to explore and plot data. The links in my answer al…
Comment: Computing allele frequencies per individual for a set of SNPs in PLINK
by
pifferdavide
▴ 100
I was able to run the --indv command successfully on a file with a bed file by simply listing the IDs in single column. However, with anoth…
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by
tomas4482
▴ 140
1. design a RNA-seq experiment specifically seuqencing non-coding RNA/circRNA sequencing. 2. subset to interested region -> extract chi…
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