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41
votes
55
replies
8.9k
views
6 follow
hash function for DNA sequences
hash hashing DNA
6.4 years ago by midox ▴ 290
27
votes
17
replies
14k
views
12 follow
Dotplot for filtered pathways result
pathways ggplot2 clusterProfiler r dotplot
8 months ago by Leite ★ 1.2k
24
votes
25
replies
4.5k
views
How to generate Beta diversity boxplot from phyloseq object?
phyloseq beta diversity metagenomics
2.0 years ago by dpc ▴ 240
23
votes
21
replies
31k
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
4.2 years ago by gaelgarcia ▴ 250
23
votes
10
replies
4.7k
views
How to predict individual ethnicity information by using hapmap data
SNP Ethnicity Hapmap
updated 15 months ago by 82k • written 4.5 years ago by ▴ 40
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
6.1 years ago by Farbod ★ 3.3k
22
votes
19
replies
2.2k
views
targets of a list of miRNAs
miRNAs RNA-Seq DEanalysis target-prediction
5.8 years ago by Angel ★ 4.1k
19
votes
43
replies
3.5k
views
Annotation of huge number of CNV files
CNV annotation TCGA
4.0 years ago by nazaninhoseinkhan ▴ 430
18
votes
4
replies
7.7k
views
How To Find Rna-Seq Data Of Published Papers?
bioinformatics next-gen rna-seq geo
9.0 years ago by user ▴ 870
18
votes
19
replies
1.4k
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
3.6 years ago by rbkh09 • 0
17
votes
13
replies
4.8k
views
7 follow
BWA: Why paired reads mapped to different chromosome?
alignment genome sequencing
5.2 years ago by lghust2011 ▴ 100
17
votes
19
replies
1.8k
views
Sorting sequences according header
software error sequence Assembly next-gen
6.0 years ago by Gian77 ▴ 60
17
votes
8
replies
1.6k
views
Number of unique authors in PubMed in last 10 years
PubMed
6.4 years ago by nejc ▴ 50
17
votes
37
replies
2.8k
views
No alias or index file found for protein database
next-gen software error sequence
updated 3.2 years ago by 20 • written 3.3 years ago by ▴ 430
16
votes
21
replies
1.3k
views
Why there are different hit for a same gene in different species
gene blast ortholog paralog
5.9 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
4.1 years ago by salamandra ▴ 500
16
votes
18
replies
2.7k
views
8 follow
Python Program to read .fasta file to .txt file
Python
updated 3.0 years ago by ★ 20k • written 3.0 years ago by • 0
16
votes
10
replies
4.4k
views
6 follow
Powerful desktop computer for genomics
next-gen sequencing ChIP-Seq RNA-Seq
6.2 years ago by Alternative ▴ 270
16
votes
8
replies
1.5k
views
8 follow
What are the most important unresolved problems in Bioinformatics?
problem unresolved bioinformatics
updated 5.8 years ago by 20 • written 5.9 years ago by ★ 2.4k
16
votes
17
replies
2.4k
views
6 follow
RNA seq pipeline
RNA-Seq
4.8 years ago by dimitrischat ▴ 180
16
votes
16
replies
2.1k
views
Using DESeq2 results for building a classifier
deseq2 RNA-Seq differentially expressed genes
4.4 years ago by Uday Rangaswamy ▴ 150
16
votes
38
replies
15k
views
Differential gene Analysis by Limma
Limma Microarray R
updated 3 months ago by 36k • written 7.5 years ago by ▴ 920
15
votes
14
replies
1.9k
views
Penalty model of BWA MEM and BOWTIE2?
RNA-Seq bwa mem bowtie2 alignment
4.6 years ago by John ▴ 240
15
votes
15
replies
23k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink SNP
updated 11 days ago by 36k • written 6.6 years ago by ▴ 180
15
votes
19
replies
1.1k
views
trimmomaric command for a fasta file?
trimmomatic
updated 4.3 years ago by 36k • written 4.3 years ago by • 0
15
votes
14
replies
1.2k
views
how can interpret these biologically weird results?
RNA-Seq
updated 18 months ago by 20 • written 4.8 years ago by ▴ 320
14
votes
17
replies
4.4k
views
HiSeq 4000 PhiX screening and removal using bbduk
spikein filtering bbmap bbduk phix
5.0 years ago by Anand Rao ▴ 520
14
votes
8
replies
4.4k
views
Unable To Replicate Splice Junction In Tophat
tophat2 bam
8.8 years ago by Dan D 7.3k
14
votes
5
replies
2.5k
views
bioinformatics basic training
genome Tutorial
updated 5 months ago by 36k • written 7.7 years ago by • 0
14
votes
16
replies
1.0k
views
Why are some mapped reads not mapped completely?
RNA-Seq mapping
updated 21 months ago by 14k • written 21 months ago by ▴ 80
14
votes
18
replies
3.8k
views
GATK Haplotype Caller
next-gen GATK haplotype caller contigs
updated 5.6 years ago by 20 • written 5.8 years ago by ▴ 50
14
votes
30
replies
2.1k
views
Download GTF/GFF annotation data for NT database, not by organism (for STAR alignment)
RNA-Seq rna-seq alignment next-gen
3.3 years ago by Malka ▴ 70
13
votes
7
replies
5.3k
views
Why some probes have "NA" for gene symbol and Entrez ID?
affymetrix microarray NA genesymbol
updated 5.7 years ago by 20 • written 5.7 years ago by ▴ 220
13
votes
16
replies
4.6k
views
6 follow
Confused about how to generate a consensus sequence after bwa
bwa samtools mpileup
3.6 years ago by DNAngel ▴ 210
13
votes
19
replies
3.7k
views
bbmerge not joining paired-end reads
bbmerge alignment
4.7 years ago by bioplanet ▴ 60
13
votes
13
replies
7.2k
views
How to do pca plot from .eigenval and .eigenvec files from Plink in R.
R SNP
updated 4.4 years ago by 102k • written 4.4 years ago by ▴ 70
13
votes
13
replies
795
views
Is reproducibility of identified variants in a gene important in Sanger sequencing?
reproducibility sanger sequencing variants
2.8 years ago by DanielC ▴ 150
13
votes
6
replies
8.8k
views
6 follow
MAF vs VAF
sequencing
4.4 years ago by lauren.wahyudi ▴ 40
13
votes
16
replies
4.5k
views
Mask or trim primer sequences in Amplicon sequencing
amplicon mask trimming fastq
5.6 years ago by Paul ★ 1.4k
13
votes
24
replies
2.8k
views
Error of bam-to-sam conversion using samtools
samtools TopHat2 RNA-Seq BAM SAM
updated 5.4 years ago by 119k • written 5.4 years ago by ▴ 480
13
votes
22
replies
8.1k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva combat batch effects
updated 4.9 years ago by 20 • written 5.1 years ago by ★ 1.2k
12
votes
28
replies
1.5k
views
Calculating the expression level of genes
Gene expression RNA-Seq R
4.2 years ago by Za ▴ 140
12
votes
13
replies
2.0k
views
Gene Expression and Systems Biology (homework)
gene homework
7.1 years ago by sarathkurichiyil • 0
12
votes
10
replies
2.0k
views
7 follow
SAM / BAM alignments
SAM BAM
5.6 years ago by John 13k
12
votes
8
replies
2.3k
views
How to change depth of sequence in RNA-seq fastq files
depth of sequence RNA-Seq
5.6 years ago by statfa ▴ 660
12
votes
17
replies
3.5k
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
4.8 years ago by anonymous1192976466 ▴ 50
12
votes
11
replies
2.6k
views
How To Get Snp Genotypes
snp genotyping
updated 10.9 years ago by 11k • written 11.3 years ago by ▴ 20
12
votes
10
replies
3.3k
views
Speed up BLASTp vs NCBI nr database
blast
6.2 years ago by biotech ▴ 560
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 8.7 years ago by 94k • written 8.7 years ago by ★ 1.4k
12
votes
14
replies
3.4k
views
bedtools intersect error?
ChIP-Seq bedtools intersect
3.5 years ago by star ▴ 290
1,000 results • Page 1 of 20
Recent Votes
Answer: How to insert dbSNP in a database?
Answer: fgsea
Answer: Finding out if a query sequence is present in a read library / bam file (blast a
C: GTF based salmon index file for GRCh38
C: GTF based salmon index file for GRCh38
Answer: Has anybody managed to install and run GroopM lately?
How to integrate multiple data sets from microarray platform prior meta-analysis?
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Recent Replies
Comment: Finding out if a query sequence is present in a read library / bam file (blast a by Pierre Lindenbaum 147k
what was the command line please ?
Comment: How to insert dbSNP in a database? by Pierre Lindenbaum 147k
2) not the same version of dbsnp, not the same build
Comment: How to insert dbSNP in a database? by magnolia • 0
Thank you! 1) I need this because I want to connect all the data I need query via SQL. 2) Thanks a lot but this file only has 200 million…
Comment: The best way to get gene lengths for 15K+ genes? by rpolicastro 9.4k
You should first ensure that calculating TPMs like this is valid for your analysis. Proper TPMs generally need to be calculated from transc…
Comment: Finding out if a query sequence is present in a read library / bam file (blast a by chronotope ▴ 10
Hey! I tried the script, but I am getting this error: > SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaultin…
Comment: Expanding reference genome with alt loci and decoy sequences by appropiate ▴ 30
My criteria for whether it makes sense would be comparing MAPQ values for alignments when using reference genome vs expanded genome. If the…
Comment: Warning - longer object length is not a multiple of shorter object length by JACKY ▴ 10
Thanks! Do you also think my genelength calculation method is slumpy? What do you think about this approach? library (EDASeq) en…
Answer: Does Cellranger filter out doublet? by ATpoint 64k
FAQ: https://kb.10xgenomics.com/hc/en-us/articles/360001074271-Does-Cell-Ranger-automatically-exclude-doublets-
Comment: Expanding reference genome with alt loci and decoy sequences by ATpoint 64k
Yes, technically you can append any sequence to the reference followed by building a new index. If that makes sense or is appropriate is a …
Comment: Warning - longer object length is not a multiple of shorter object length by Michael Dondrup 52k
for example edgeR see https://support.bioconductor.org/p/64585/ Refer to https://www.biostars.org/p/115674/ , https://www.ncbi.nlm.nih.go…
Answer: How to insert dbSNP in a database? by Pierre Lindenbaum 147k
1) why do you need this ? 2) you can always upload the UCSC dbsnp files. ex.: http://hgdownload.cse.ucsc.edu/goldenpath/hg19/databas…
Comment: Finding out if a query sequence is present in a read library / bam file (blast a by chronotope ▴ 10
thanks! I will try it out today
Comment: getting RPKM and VST using DEseq2 package by andrew.j.skelton73 6.4k
Check out [this][1] discussion on gene length in DESeq2. [1]: https://support.bioconductor.org/p/67131/
Comment: Warning - longer object length is not a multiple of shorter object length by JACKY ▴ 10
A proven Bioconductor package you mean using a package for normalization? If so, is there any package you recommend ?
Answer: MAKER AED score by lei • 0
Did you adjust this setting in the maker_opts.ctl file? >pred_stats=1 #report AED and QI statistics for all predictions as well as models
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