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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
7.2 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
910
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
19
replies
2.2k
views
Sorting sequences according header
software error
sequence
Assembly
next-gen
6.8 years ago by
Gian77
▴ 60
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
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
2.5k
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
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
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
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
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
13
replies
8.1k
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
5.7k
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
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
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
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
19
replies
4.5k
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
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
6
replies
10k
views
6 follow
MAF vs VAF
sequencing
5.2 years ago by
lauren.wahyudi
▴ 40
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
13
replies
2.2k
views
Gene Expression and Systems Biology (homework)
gene
homework
updated 6 months ago by
Ram
39k • written 7.9 years ago by
sarathkurichiyil
• 0
12
votes
10
replies
2.4k
views
7 follow
SAM / BAM alignments
SAM
BAM
6.4 years ago by
John
13k
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
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
1,000 results • Page
1 of 20
Recent Votes
Tools To Calculate Average Coverage For A Bam File?
Comment: conda: command not found: gatk.
Answer: Finding Enhancers using Genomation library
Comment: If I execute "AddOrReplaceReadGroups" on a sarted and duplicate-marked .bam fil
Answer: Extract variants/SNPs with T>G substitution from a VCF file
Comment: ChatGPT optimized for bioinformatics questions
Comment: ChatGPT optimized for bioinformatics questions
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Recent Replies
Comment: conda: command not found: gatk.
by
GenoMax
130k
Follow directions provided by `GATK` project: https://gatk.broadinstitute.org/hc/en-us/articles/360035889851--How-to-Install-and-use-Conda-…
Answer: What's the correct way to store bam record in a vector and free them?
by
Pierre Lindenbaum
155k
You should allocate a new pointer for each SAM record. I would do something like this (not tested): ``` std::vector<bam1_t*> record_list…
Comment: Creating a local version of Clustered NR database
by
GenoMax
130k
Thanks for those stats. So using clustered `nr` will still require significant hardware. Though this will save time as well.
Comment: Can I send my PyMol results to a web-page as a result for a submitted query? If
by
Aatif Hashmi
• 0
Basically I only want to show bases with disulphide bonds. like imagine I have a disulphide bond at 68 cys residue along with 145 cys. I …
Answer: How do I specify the Recalibration_data.table for "PrintReads" in GATK 4.3, if t
by
Pierre Lindenbaum
155k
do you want ApplyBQSR "Apply base quality score recalibration " ? https://gatk.broadinstitute.org/hc/en-us/articles/360036856671-ApplyBQSR
Comment: target vs. bait BED files for Illumina WES
by
Sounkou-bioinfo
• 0
Hi @jacorvar , did you find the answer to that question ?
Comment: ChatGPT optimized for bioinformatics questions
by
Dr William Klubinski
▴ 100
That's an excellent point. A significant number of students are engaged in academic misconduct due to the use of fabricated references and …
Comment: Filtering content in heatmap to highest values
by
Papyrus
★ 2.5k
You mean something like this? depends on how you define "top" row or column # Create example (it is a data.table) ListerTFHeat <- …
Comment: conda: command not found: gatk.
by
666billgaytes
▴ 10
Could there be an issue with your OS? I find a lot of colleagues having problems with Mac OS and much less if none at all on Windows.
Comment: ChatGPT optimized for bioinformatics questions
by
Dr William Klubinski
▴ 100
Great initiative :D
Answer: Extract variants/SNPs with T>G substitution from a VCF file
by
4galaxy77
2.7k
Use ```bcftools view``` with the `-i` flag for including variants. ``` bcftools view -i'REF=="T" & AlT == "G"' ```
Comment: A question about the raw RNA-seq processing workflow
by
Dr William Klubinski
▴ 100
Hi there, the `Segmentation fault (core dumped)` seems to be related to memory issues. I would check the `core dump` that has been created …
Comment: Ensembl vep singularity
by
Ben_Ensembl
★ 2.2k
Hi Kiran - there is a description of downloading and running VEP with Singularity 3.5+ in the following blog post: https://www.ensembl.inf…
Comment: conda: command not found: gatk.
by
bestone
▴ 20
Is there anyone who can help me with this?
Comment: conda: command not found: gatk.
by
bestone
▴ 20
oops I didn't know I was going to evaluate them there, thanks for the warning, now I will evaluate them all. pls, could you pls with this i…
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