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Tutorial: Video: Visualization of whole genome DNA methylation data in IGB
Bismark BS-Seq RNA-Seq IGB
updated 18 months ago by 41k • written 8.7 years ago by ▴ 860
15
votes
3
replies
4.5k
views
Tutorial: NCBI blast tutorial
ncbi blast
updated 8 months ago by 41k • written 7.6 years ago by 11k
0
votes
3
replies
51k
views
Tutorial: Installation VMD on LINUX_64
gromacs VMD
updated 8 months ago by 41k • written 7.5 years ago by ▴ 10
0
votes
3
replies
2.5k
views
Tutorial: Automatic Primer Design
Assembly sequence
updated 15 months ago by 41k • written 8.1 years ago by ▴ 40
10
votes
3
replies
4.3k
views
Tutorial: Video: Alternative Splicing and Primer Design
RNA-Seq IGB
updated 10 months ago by 41k • written 9.2 years ago by ▴ 860
4
votes
3
replies
4.4k
views
Tutorial: How to get full taxonomy classification using taxize and myTAI
taxonomy R
updated 8 months ago by 41k • written 5.7 years ago by ★ 3.9k
5
votes
3
replies
4.1k
views
Tutorial: Chip Seq Review Papers
chip-seq
updated 9 months ago by 41k • written 11.0 years ago by ▴ 80
72
votes
3
replies
37k
views
Tutorial: Revisiting the FastQC read duplication report
fastqc
updated 2.1 years ago by 41k • written 9.4 years ago by 99k
2
votes
3
replies
1.9k
views
Tutorial: Help demonstrate reproducibility in bioinformatics with the GA4GH's tool execution Challenge
GA4GH Docker CWL Rabix
updated 7 months ago by 41k • written 6.8 years ago by ▴ 20
13
votes
3
replies
14k
views
Tutorial: Plotting the coverage and depth (Y-axis) statistics of a bam file along the genome (X-axis), using Samtools, awk and R.
genome plot coverage samtools
updated 3 months ago by ▴ 20 • written 6.7 years ago by ★ 1.6k
44
votes
3
replies
12k
views
Tutorial: A Wet-Lab Guide to 'what I wish I had known' for Computational Biology
bioinformatics computational-biology
updated 8 months ago by 41k • written 7.7 years ago by ★ 3.2k
5
votes
3
replies
5.1k
views
Tutorial: bam2rpkm by bedtools
bam RNA-Seq bedtools rpkm
updated 8 months ago by • 0 • written 6.1 years ago by ▴ 130
3
votes
3
replies
2.5k
views
Tutorial: Generating count matrix for STAR counts in GDC v32.0 for RNA-Seq
GDC TCGABiolinks STAR
updated 9 months ago by 41k • written 20 months ago by ★ 3.3k
19
votes
3
replies
13k
views
Tutorial: bedGraphToBigWig Tutorial and Report
bedGraphToBigWig
updated 17 months ago by 41k • written 7.8 years ago by ★ 9.3k
9
votes
3
replies
4.1k
views
Tutorial: Ht Sequence Analysis With R And Bioconductor By The Bioinformatics Center At Uc Riverside
bioconductor
updated 9 months ago by 41k • written 11.3 years ago by 99k
51
votes
3
replies
22k
views
Tutorial: Sam File Format - Lesser Known Tips And Tricks
sam
updated 9 months ago by 41k • written 10.9 years ago by ▴ 300
12
votes
2
replies
1.2k
views
Tutorial: Factors in R - How do they work, and how did I break my data?
R
updated 8 months ago by 41k • written 2.7 years ago by 12k
15
votes
2
replies
2.9k
views
Tutorial: Introduction to bedtools.
bedtools
updated 9 months ago by 41k • written 9.1 years ago by 12k
6
votes
2
replies
3.7k
views
Tutorial: How to extract fastq files from SRA data that contains both paired and unpaired reads
fastq-dump sra
updated 8 months ago by 41k • written 7.7 years ago by ▴ 840
5
votes
2
replies
3.0k
views
Tutorial: Get GC Content from UCSC with perl script (mysql)
myql ucsc gc-content perl
updated 7 months ago by 41k • written 6.7 years ago by ★ 9.3k
6
votes
2
replies
4.0k
views
Tutorial: GATK method for filtering vcf lines using GT values at all or multisample level.
genome vcf genotype variant-filtration
updated 6 months ago by 41k • written 6.5 years ago by ★ 1.6k
4
votes
2
replies
2.5k
views
Tutorial: Building mosdepth on macOS
nim mosdepth
updated 3 months ago by 136k • written 3.6 years ago by 78k
8
votes
2
replies
6.5k
views
Tutorial: Troubleshooting issues with SURPI pipeline for pathogen identification from complex metagenomic NGS data.
metagenomics clinical-genomics
updated 22 months ago by 41k • written 9.1 years ago by 12k
0
votes
2
replies
5.2k
views
Tutorial: Install AMOS on Ubuntu 13.10
sequencing alignment software-error next-gen
updated 2.1 years ago by 41k • written 9.4 years ago by 9.7k
1
vote
2
replies
638
views
Tutorial: How to ask computational biology questions
computational-biology
updated 5 months ago by 41k • written 5 months ago by ★ 3.6k
14
votes
2
replies
2.3k
views
Tutorial: Exploring OpenSNP - an RMarkdown report on crowdsourced genotypes and phenotypes
SNP R
updated 8 months ago by 41k • written 7.7 years ago by 22k
7
votes
2
replies
1.6k
views
Tutorial: A tale of two heatmap function
clustering heatmap
updated 8 months ago by 41k • written 7.2 years ago by ★ 3.6k
6
votes
2
replies
2.6k
views
Tutorial: Tutorial Bioinformatics Static Website
website
updated 9 months ago by 41k • written 9.9 years ago by ▴ 610
7
votes
2
replies
11k
views
Tutorial: Howto use NCBI programs behind a HTTP proxy
blast-plus HTTP-proxy SRA-toolkit
updated 17 months ago by 41k • written 7.8 years ago by ★ 1.8k
7
votes
2
replies
1.8k
views
Tutorial: Introduction to Human Genomics for Clinical Informaticists
genome
updated 6 months ago by 41k • written 6.3 years ago by ▴ 90
3
votes
2
replies
676
views
Tutorial: How to use UCSC genome browser to check the transcription factor binding at your favorite gene
UCSC transcription factor ChIP-seq
4 months ago by Ming Tommy Tang ★ 3.6k
20
votes
2
replies
7.8k
views
Tutorial: Creating a karyotype plot with genes using karyoploteR
karyoploteR visualization R genome
updated 6 months ago by 41k • written 6.0 years ago by ★ 3.4k
22
votes
2
replies
5.8k
views
Tutorial: Use a workflow management tool to manage your computational pipelines
workflow-management snakemake pipeline
updated 8 months ago by 41k • written 7.1 years ago by ★ 2.1k
3
votes
2
replies
5.2k
views
Tutorial: Reorder Vcf Files
vcf
updated 9 months ago by 41k • written 10.6 years ago by ▴ 60
0
votes
2
replies
2.3k
views
Tutorial: COURSE: NGS variant analysis and interpretation for translational research
CNIO course translational
updated 8 months ago by 41k • written 7.3 years ago by ▴ 190
3
votes
2
replies
2.5k
views
Tutorial: Continuing Education (Pipelines): Best blogs, Online Lectures, Workshops, etc..
conferences Workshops
updated 6 months ago by 41k • written 6.6 years ago by ▴ 100
18
votes
2
replies
5.8k
views
Tutorial: Update kraken databases
database kraken k-mer python
updated 6 months ago by 41k • written 6.6 years ago by 5.3k
5
votes
2
replies
1.6k
views
Tutorial: ENCODE 2016: Research Applications and Users Meeting
ChIP-Seq next-gen ENCODE
updated 8 months ago by 41k • written 7.5 years ago by ★ 1.1k
10
votes
2
replies
3.6k
views
Tutorial: Graph visualization with igraph in R
Visualization igraph Graph R Network
updated 7 months ago by 41k • written 6.7 years ago by 26k
60
votes
2
replies
7.2k
views
Tutorial: Table Of Contents To All Review Paper Compilations On Biostar
papers
updated 9 months ago by 41k • written 11.3 years ago by 99k
0
votes
2
replies
2.5k
views
Tutorial: Webinar on 'An integrated RNA and DNA approach to unravel genetic regulation in cancer' on 25 Feb
SNP cancer gene-regulation multiomics rna-seq
updated 20 months ago by 41k • written 8.8 years ago by ▴ 70
3
votes
2
replies
2.4k
views
Tutorial: Running fastq_screen on your data
fastqscreen
20 months ago by rohitsatyam102 ▴ 780
1
vote
2
replies
1.3k
views
Tutorial: ViennaRNA package installation in Windows
windows rna mfold viennarna
updated 5 months ago by 41k • written 14 months ago by ▴ 20
4
votes
2
replies
1.9k
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation rRNA RNAmmer Genome
4 months ago by Dr.Animo ▴ 80
4
votes
2
replies
7.1k
views
Tutorial: Analyzing Genomewide Association Study Data: A Tutorial Using Plink
plink gwas
updated 9 months ago by 41k • written 11.6 years ago by 99k
2
votes
2
replies
1.9k
views
Tutorial: Human mitochondrial DNA annotation in SnpEff
chrMT SNP snpEff
updated 8 months ago by 41k • written 3.4 years ago by 3.2k
4
votes
2
replies
2.3k
views
Tutorial: Apply beagle5.0 to make imputation and phasing under CentOS and PBS
beagle5.0 beagle
updated 8 months ago by 41k • written 4.5 years ago by ★ 9.3k
14
votes
2
replies
6.3k
views
Tutorial: ChIP-seq analysis tutorial
ChIP-Seq
updated 8 months ago by 41k • written 8.3 years ago by ★ 3.6k
21
votes
2
replies
5.2k
views
Tutorial: Extracting genomic feature sequences from GTF/GFF files with AGAT
extract GTF GFF sequence
updated 15 months ago by ▴ 40 • written 2.6 years ago by 8.4k
1
vote
2
replies
3.2k
views
Tutorial: Standalone BLAST error: UnexpectedTagClassByte
software-error blast
updated 13 months ago by 41k • written 8.4 years ago by ▴ 10
384 results • Page 4 of 8
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Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out
Answer: How to query 1000 genomes project VCF files for specific regions without downloa
Answer: Issue softclipping reads when they belong and don't belong to a common amplicon
Answer: Issue softclipping reads when they belong and don't belong to a common amplicon
Answer: how to remove multiple columns from a file in R
Answer: how to remove multiple columns from a file in R
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Comment: SQL request from NCBI metadata and stat_analysis tables by marie.harmel • 0
Thank you for your answer but unfortunately I tried it and it makes the same kind of ouptut as mine, with multtiple new (false) lines (spl…
Comment: Normalization of RNA captureSeq data (<20 genes captured) by ATpoint 78k
What is the question exactly? With only 20 genes you basically **must** use the spike-ins as that few genes do not really allow to normaliz…
Comment: Building reference dbSNP file using WGS samples by analyst ▴ 10
Dear [Brian][1] I realized that problem is with callvariants.sh script because when I called variants using freebayes I did not find aforem…
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out by analyst ▴ 10
Its bbmap tool callvariants.sh. I think you are right because I did not get such error when I called variants through freebayes.
Answer: Efficient way of calculating the number of mismatches between two sets of sequen by j.gleixner • 0
Since all your sequences have the same length (say M) and you are only looking concerned with hamming distance you can encode your sequence…
Comment: Where to download excel file to include major human disease, prevalence and inci by GenoMax 136k
ChatGPT says Disease Prevalence Approximate Number of Cases (Worldwide) Cardiovascular Diseases High Over 17 million deaths annual…
Comment: Where to download excel file to include major human disease, prevalence and inci by Pierre Lindenbaum 158k
using wikidata: https://query.wikidata.org/sparql?query=%0ASELECT%20%3Fitem%20%3FitemLabel%20%3FitemDescription%20%3Fprevalence%20%3Fdoid%0…
Comment: Opinion on miRNA pipeline by ju_ra • 0
Thank you very much! I see you decided to go for Bowtie as aligner. Do you see any issue in using STAR (as a splice aware reader technicall…
Answer: How to avoid missannotated GO terms? by Elisabeth Gasteiger ★ 2.3k
Please contact the UniProt helpdesk whenever you find such annotations, especially in these cases where the GO evidence/source tag says "Un…
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out by Pierre Lindenbaum 158k
again, it's a problem with the variant caller, which is ?
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out by analyst ▴ 10
Not only opposite case but same case nucleotides are also present in vcf fle. ![enter image description here][1] [1]: /media/images/4…
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out by analyst ▴ 10
Yes [Pierre][1] there is lower case **g** in **REF** and upper case **G** in **ALT** field. My question is that why variant caller is calli…
Answer: gatk SelectVariants is giving error while extracting SNPs out of vcf file by Pierre Lindenbaum 158k
This is an error in your input vcf file. The REF allele MUST be différent from the ALT allele.
Comment: gatk SelectVariants is giving error while extracting SNPs out of vcf file by analyst ▴ 10
I observed that my reference genomic fasta file contains both lower case and upper case nucleotides. Do I need to convert lower case nucle…
Comment: Building reference dbSNP file using WGS samples by analyst ▴ 10
I observed that both lower and upper cases are present in reference fasta file. Is bbtool case sensitive that while calling variants it con…
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