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1,000 results • Page 1 of 20
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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 • 0 • written 5.1 years ago by ▴ 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 85k • written 5.2 years ago by ▴ 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 39k • written 6.9 years ago by ★ 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 39k • written 7.4 years ago by ▴ 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 39k • written 9.8 years ago by ▴ 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 39k • written 4.4 years ago by • 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 20 • written 4.1 years ago by ▴ 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 ★ 23k • written 3.8 years ago by • 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 39k • written 6.6 years ago by ★ 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 39k • written 8.3 years ago by ▴ 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 20 • written 5.6 years ago by ▴ 330
15
votes
19
replies
1.4k
views
trimmomaric command for a fasta file?
trimmomatic
updated 5.1 years ago by 39k • written 5.1 years ago by • 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 20 • written 6.6 years ago by ▴ 50
14
votes
5
replies
2.8k
views
bioinformatics basic training
genome
updated 10 weeks ago by 39k • written 8.5 years ago by • 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 14k • written 2.5 years ago by ▴ 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 20 • written 6.5 years ago by ▴ 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 20 • written 5.9 years ago by ★ 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 103k • written 5.2 years ago by ▴ 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 129k • written 6.2 years ago by ▴ 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 39k • written 7.9 years ago by • 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 98k • written 9.5 years ago by ★ 1.4k
12
votes
11
replies
2.8k
views
How To Get Snp Genotypes
snp genotyping
updated 11.7 years ago by 11k • written 12.1 years ago by ▴ 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 1 of 20
Recent Votes
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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