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1,000 results • Page
1 of 20
Sort: Votes
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Views
Votes
Replies
41
votes
55
replies
10k
views
6 follow
hash function for DNA sequences
hash
hashing
DNA
7.2 years ago by
midox
▴ 290
27
votes
17
replies
18k
views
12 follow
Dotplot for filtered pathways result
pathways
ggplot2
clusterProfiler
r
dotplot
18 months ago by
Leite
★ 1.2k
24
votes
25
replies
6.2k
views
How to generate Beta diversity boxplot from phyloseq object?
phyloseq
beta diversity
metagenomics
2.9 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 6 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 5.3 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 8 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
6.7 years ago by
fi1d18
★ 4.2k
20
votes
17
replies
5.2k
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 10 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
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 6 months ago by
Ram
39k • written 4.4 years ago by
rbkh09
• 0
18
votes
7
replies
908
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
18
votes
4
replies
8.2k
views
How To Find Rna-Seq Data Of Published Papers?
geo
next-gen
RNA-seq
updated 3 months ago by
Ram
39k • written 9.8 years ago by
user
▴ 930
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
6.1 years ago by
lghust2011
▴ 100
17
votes
19
replies
2.2k
views
Sorting sequences according header
software error
sequence
Assembly
next-gen
6.8 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 4.2 years ago by
williamsbrian5064
▴ 470
16
votes
14
replies
14k
views
Which truseq trimmomatic adapters file to use when removing truseq adapters?
adapters
trimmomatic
RNA-seq
5.0 years ago by
salamandra
▴ 540
16
votes
18
replies
4.2k
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
6.7 years ago by
Farbod
★ 3.4k
16
votes
17
replies
2.8k
views
6 follow
RNA seq pipeline
RNA-Seq
5.6 years ago by
dimitrischat
▴ 180
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
8
replies
1.7k
views
8 follow
What are the most important unresolved problems in Bioinformatics?
bioinformatics
updated 8 weeks ago by
Ram
39k • written 6.7 years ago by
chen
★ 2.4k
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
10
replies
4.9k
views
6 follow
Powerful desktop computer for genomics
next-gen
sequencing
ChIP-Seq
RNA-Seq
7.0 years ago by
Alternative
▴ 270
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 2.4 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
9.7 years ago by
Dan D
7.4k
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
16
replies
1.4k
views
Why are some mapped reads not mapped completely?
RNA-Seq
mapping
updated 2.6 years ago by
lieven.sterck
14k • written 2.6 years ago by
utsafar
▴ 80
14
votes
5
replies
2.8k
views
bioinformatics basic training
genome
updated 12 weeks ago by
Ram
39k • written 8.5 years ago by
f.muoghalu
• 0
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
13
votes
7
replies
5.9k
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 6.6 years ago by
Raheleh
▴ 250
13
votes
11
replies
5.7k
views
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
RNA-Seq
QC
4.6 years ago by
jackgrayner
▴ 80
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
13
replies
8.0k
views
How to do pca plot from .eigenval and .eigenvec files from Plink in R.
R
SNP
updated 5.3 years ago by
Devon Ryan
103k • written 5.3 years ago by
amitgourav.ghosh12
▴ 70
13
votes
16
replies
5.2k
views
Mask or trim primer sequences in Amplicon sequencing
amplicon
mask
trimming
fastq
6.4 years ago by
Paul
★ 1.5k
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
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
130k • written 6.2 years ago by
Gary
▴ 480
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
6
replies
10k
views
6 follow
MAF vs VAF
sequencing
5.2 years ago by
lauren.wahyudi
▴ 40
13
votes
13
replies
13k
views
How to interpret Per sequence GC content module in FastQC for RNA-seq data?
RNA-Seq
FastQC
QC
GC-content
3.8 years ago by
Arindam Ghosh
▴ 500
13
votes
19
replies
4.5k
views
bbmerge not joining paired-end reads
bbmerge
alignment
5.5 years ago by
bioplanet
▴ 60
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
14
replies
4.6k
views
bedtools intersect error?
ChIP-Seq
bedtools
intersect
4.3 years ago by
star
▴ 340
12
votes
17
replies
4.0k
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
5.7 years ago by
anonymous1192976466
▴ 50
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
4
replies
504
views
Annotating TSS: By Transcript or by Gene? Code Validation Help Needed!
genome
bed
transcript
TSS
23 days ago by
Rafael Soler
★ 1.2k
12
votes
11
replies
2.8k
views
How To Get Snp Genotypes
snp
genotyping
updated 11.8 years ago by
Lars Juhl Jensen
11k • written 12.2 years ago by
Pri
▴ 20
1,000 results • Page
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Recent Votes
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
A: Mouse promoter regions
Answer: How to get information about promoter from bulk-RNAseq?
A: Extracting Flanking Regions across TSS using R scripts
A: Mouse promoter regions
A: Finding zebrafish promoters ENSEMBL
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Comment: How to get information about promoter from bulk-RNAseq?
by
camillab.
▴ 130
and what about enhancer? is it possible to do it from a bulk-RNAseq?
Comment: How to get information about promoter from bulk-RNAseq?
by
camillab.
▴ 130
yes! clearly the terminology on my side needs to improved!
Comment: How to get information about promoter from bulk-RNAseq?
by
rpolicastro
12k
Generally speaking, most promoters only initiate transcription for a single gene, with a single gene potentially having multiple promoters …
Answer: How to get information about promoter from bulk-RNAseq?
by
Trivas
★ 1.2k
I'd probably select the genes of interest from your bulk RNA-seq results then use the UCSC table browser to get the sequence upstream of th…
Comment: How to add annotation columns with specific colors to the heatmap?
by
Ram
39k
Show us your exact code - it is quite easy to tweak colors in ComplexHeatmap with the `col=` argument.
Comment: VCF file CSQ flag
by
Ram
39k
True, but it's not technically impossible to annotate GVCFs, which is why I did not address that point.
Comment: Creating a local version of Clustered NR database
by
PeterC_NCBI
▴ 260
@genomax Sorry for the delay in reply. We're still working out the details of what exactly to provide. One idea is to provide just the rep…
Comment: Shannon's Entropy by Sliding Window in R
by
rohitsatyam102
▴ 690
Hi Were u able to achieve this?
Comment: Differences in GTF files hg19 and hg38
by
GenoMax
130k
Since this is not an answer to the original question do not add it as such. I moved your last comment to the correct spot it should have be…
Comment: VCF file CSQ flag
by
Pierre Lindenbaum
154k
if your talking about the gvcf produced by HaplotypeCaller with ERC=GVCF, you don't annote g.vcf files , you must first merge the g.vcf.f…
Comment: [python]sklearn.ensemble.RandomForestClassifier(TypeError: string indices must b
by
Ram
39k
https://www.biostars.org/u/127538/ : Please delete this question or it will be deleted by moderators in a few days.
Comment: VCF file CSQ flag
by
Ram
39k
A gvcf files has blocks for both variant loci and non-variant loci, so you won't see a CSQ for each record, only for those variant loci wit…
Comment: Differences in GTF files hg19 and hg38
by
heureuse
• 0
Thank you very much. I get it from UCSC.
Comment: [python]sklearn.ensemble.RandomForestClassifier(TypeError: string indices must b
by
Arup Ghosh
3.2k
This post does not fit the theme of this forum.
Comment: CellRanger problem
by
Arup Ghosh
3.2k
Try with atleast 32 GB of Memory rather than 16 GB specified by `limitGenomeGenerateRAM` option.
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