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23
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22
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37k
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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 3 months ago by • 0 • written 4.9 years ago by ▴ 250
4
votes
4
replies
33k
views
How to convert a URL into a DOI programmatically
pubmed doi url
written 6.5 years ago by ▴ 100
19
votes
15
replies
25k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink SNP
updated 7 months ago by 38k • written 7.2 years ago by ▴ 180
4
votes
13
replies
24k
views
6 follow
[main_samview] fail to read the header from sample.bam
alignment
updated 8 months ago by • 0 • written 5.0 years ago by ▴ 20
4
votes
6
replies
23k
views
terminate called after throwing an instance of 'std::bad_alloc?
bedtools linux data
3.9 years ago by star ▴ 330
1
vote
3
replies
23k
views
How to extract vcf.gz and vcf.gz.tbi
SNP sequence gene
updated 4.7 years ago by 153k • written 4.7 years ago by ▴ 20
3
votes
4
replies
21k
views
Using nr database for BLAST search
nr database blast blastp
updated 6.5 years ago by 20 • written 6.7 years ago by ▴ 20
9
votes
4
replies
20k
views
What is the definition of "read depth" vs "coverage"? (again...)
coverage depth read depth
5.9 years ago by ariel.balter ▴ 190
2
votes
4
replies
20k
views
Error in file(file, "rt") : cannot open the connection
R MicroRNA TXT FORMAT
updated 6.9 years ago by 126k • written 6.9 years ago by • 0
1
vote
5
replies
17k
views
Calculating the sequence similarity and percentage of matched sequences
alignment sequence
updated 5.3 years ago by • 0 • written 5.4 years ago by ▴ 10
7
votes
16
replies
17k
views
featureCounts: Low percentage of assigned fragments
RNA-Seq rna-seq
6.6 years ago by aggregatibacter ▴ 170
27
votes
17
replies
16k
views
12 follow
Dotplot for filtered pathways result
pathways ggplot2 clusterProfiler r dotplot
15 months ago by Leite ★ 1.2k
2
votes
8
replies
16k
views
Using vcfutils.pl command
alignment
updated 11 months ago by 38k • written 8.1 years ago by ▴ 40
2
votes
10
replies
16k
views
How do you use the Aspera ascp command?
aspera gigascience gigaDb
updated 18 months ago by 38k • written 7.4 years ago by ▴ 940
16
votes
38
replies
15k
views
Differential gene Analysis by Limma
Limma Microarray R
updated 10 months ago by 38k • written 8.1 years ago by ▴ 920
2
votes
13
replies
15k
views
convert text file to fasta file
blast
updated 6.6 years ago by 12k • written 6.6 years ago by ▴ 30
6
votes
2
replies
15k
views
Pacbio Ccs Vs Subreads Explained ?
updated 8.9 years ago by 20 • written 9.4 years ago by ▴ 40
0
votes
8
replies
15k
views
find ORF in sequence python
sequence
updated 6.2 years ago by ★ 3.9k • written 6.2 years ago by ▴ 120
2
votes
2
replies
15k
views
How to calculate the insert size for Paired-end reads
SSPACE insert-size
6.7 years ago by Ric ▴ 430
2
votes
3
replies
14k
views
Subsetting - Raw Counts from Seurat Object
seurat raw counts RNA-Seq
2.9 years ago by David_emir ▴ 460
4
votes
10
replies
14k
views
How to plot a multiple line graph with Mean and Std Error for following dataset?
R
updated 4.9 years ago by 126k • written 4.9 years ago by ▴ 720
0
votes
3
replies
14k
views
How to choose a TPM cut-off point
RNA-Seq transcript tpm
updated 7 months ago by 38k • written 7.4 years ago by ▴ 10
0
votes
3
replies
14k
views
Error in (function (classes, fdef, mtable): unable to find an inherited method for function ‘annotation’ for signature ‘"character
inSilicoMerging
8.8 years ago by ira_grich • 0
2
votes
4
replies
14k
views
TRIMMOMATRIC Nextera trimming
next-gen
updated 5 months ago by 38k • written 7.6 years ago by ▴ 10
16
votes
14
replies
14k
views
Which truseq trimmomatic adapters file to use when removing truseq adapters?
adapters trimmomatic RNA-seq
4.7 years ago by salamandra ▴ 530
5
votes
4
replies
14k
views
glmnet package lasso error
glmnet lasso multilinear regression
5.0 years ago by demoraesdiogo2017 ▴ 90
3
votes
1
reply
13k
views
How do you normalize Transcript per Million TPM to compare between samples ?
RNA-Seq TPM STAR salmon quantification
6.2 years ago by ZheFrench ▴ 500
1
vote
8
replies
13k
views
HTSeq-count high number of no_feature
htseq-count rna-seq
updated 11 months ago by 38k • written 8.1 years ago by ▴ 80
8
votes
5
replies
13k
views
The comparison between HISAT2 and Tophat2
RNA-Seq Tophat2 HISAT2
updated 4.5 years ago by 38k • written 7.1 years ago by ▴ 50
9
votes
13
replies
13k
views
GC Content of Fasta file --- Python Help
sequence
6.1 years ago by Patrick Brennan ▴ 50
7
votes
4
replies
13k
views
Use of if-else statement in snakemake rule
snakemake if-else python
updated 3.3 years ago by • 0 • written 5.7 years ago by ▴ 130
0
votes
2
replies
13k
views
Error in -delete: invalid argument to unary operator
RNA-Seq R
3.1 years ago by ovariohisterectomia ▴ 40
1
vote
5
replies
12k
views
pheatmap: how to use legend information as row annotation?
R pheatmap legend annotation
4.9 years ago by n85825 • 0
3
votes
8
replies
12k
views
Error when running pheatmap
pheatmap Error in hclust
4.0 years ago by luzglongoria ▴ 40
6
votes
13
replies
12k
views
Fastq file is truncated error message
RNA-Seq error fastq
6.8 years ago by rob.costa1234 ▴ 310
0
votes
2
replies
12k
views
How to download pfam database
sequence
updated 6.2 years ago by 9.5k • written 6.2 years ago by ▴ 30
6
votes
13
replies
12k
views
Showing FDR and log2FC in Volcano plot using R
R RNA-Seq volcano plot
updated 3.8 years ago by 11k • written 5.3 years ago by ★ 3.4k
0
votes
4
replies
12k
views
Unable to install XLconnect package in R studio version 3.2.1
R
updated 5 months ago by 38k • written 7.6 years ago by ▴ 10
4
votes
1
reply
12k
views
Converting BigBed to Bed format
Installing BigFile Support
7.8 years ago by sumaira.zaman10 ▴ 20
3
votes
11
replies
12k
views
What is the acceptable % of reads that map to no feature (in RNASeq)?
htseq RNA-Seq STAR
updated 11 months ago by 38k • written 8.2 years ago by ▴ 120
2
votes
4
replies
12k
views
Run BLAST on Linux terminal
ncbi nBLAST linux blast
updated 6 months ago by 38k • written 7.5 years ago by ★ 1.2k
9
votes
13
replies
12k
views
How to interpret Per sequence GC content module in FastQC for RNA-seq data?
RNA-Seq FastQC QC GC-content
3.6 years ago by Arindam Ghosh ▴ 470
9
votes
13
replies
12k
views
Sort bam file by coordinates using samtools
sequencing next-gen gene rna-seq Tool
updated 4.5 years ago by 15k • written 4.5 years ago by ▴ 30
4
votes
18
replies
12k
views
Alignment with BWA and SAMtools
BWA SAM-file SAMtools
updated 2.4 years ago by 20 • written 4.6 years ago by ▴ 30
1
vote
2
replies
12k
views
kart file in prefetch
rna-seq
updated 6.4 years ago by 20 • written 6.6 years ago by ▴ 20
0
votes
1
reply
11k
views
PLINK 1.9 - Converting PED/MAP to BED/BIM/FAM with missing values
plink
updated 6.6 years ago by 20 • written 6.7 years ago by ▴ 80
0
votes
3
replies
11k
views
Extracting Specific Columns from Multiple Files & Writing to File Python
python file-handeling
6.8 years ago by BioICoder ▴ 40
0
votes
2
replies
11k
views
GSEA error - After pruning, none of the gene sets passed size thresholds
RNA-Seq GSEA gene genome
updated 3.6 years ago by ▴ 330 • written 3.6 years ago by • 0
4
votes
12
replies
11k
views
STAR alignment error- Segmentation fault (core dumped)
alignment software error RNA-Seq STAR
4.7 years ago by EagleEye 7.4k
3
votes
2
replies
11k
views
ExAC PLI score calculation
DNA-Seq
6.1 years ago by jonessara770 ▴ 240
1,000 results • Page 1 of 20
Recent Votes
The Biostar Handbook. A bioinformatics e-book for beginners.
Converting mapped + unmapped BAM files to raw FASTQ (RNA-seq data)
Converting mapped + unmapped BAM files to raw FASTQ (RNA-seq data)
Comment: GATK GenotypeGVCFs explain
Comment: Pig Reference Genome
Network plot from expression data in R using igraph
Network plot from expression data in R using igraph
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Comment: GATK GenotypeGVCFs explain by raphael.B ▴ 270
It limits the operation to some genomic regions given as parameter
Comment: GATK GenotypeGVCFs explain by Sarah ▴ 30
what does the option L
Comment: GATK GenotypeGVCFs explain by Pierre Lindenbaum 153k
GenotypeGVCFs takes a set of GVCF files called with HaplotyperCaler and output a VCF file.
Answer: TCGA Methylation Data and Gene Mapping by Basti ★ 1.4k
CpGs may be annotated to more than >1 gene simply because gene regions overlap on the genome. If you want to associate each gene to a me…
Comment: Circos plot by Fabio Marroni ★ 3.0k
Please give a look to [this post][1] for increasing the probability to get an answer. If I may add some needed info: 1. What exactly do y…
Comment: Trying to install Roary with Conda results in error message by tobiwan ▴ 10
Wow, thank you so much for your explanation! My conda channel is indeed set to strict priority. Should packages with different dependencie…
Comment: FeatureCounts >edgeR > GO by Basti ★ 1.4k
You can use BioMart to convert your "gene-IDs" to gene symbols, but you need to specify from which database your gene identifiers come from
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If you search "DAVID dotplot" on this forum, you have many answers to your question. Note that you can also perform DAVID Functional Enrich…
Answer: How to implement this two-stage one-to-many workflow using WDL? by Pierre Lindenbaum 153k
nottested, something like: ``` version 1.0 workflow BIOSTAR { call FIRST { } scatter (F in FIRST.each_F)…
Answer: Databases to check variant pathogenicity by AtenaLia ▴ 20
You can try https://genebe.net , it is similar to Varsome though...
Answer: ACMG assignment tools by AtenaLia ▴ 20
Hi, free ACMG implementation without restrictions can be found at https://genebe.net . AFAIK there is also a free API coming.
Comment: Bad quality fastq files for analysis by Gene_MMP8 ▴ 220
I don't have the data available. I want to identify such datasets. The overall aim is to determine what factors influence fastq data qualit…
Comment: mrbayes segmentation fault by Mensur Dlakic ★ 23k
I don't know what exactly the error message means. What I can tell you is that a burn-in of 2500 generations is absolutely inadequate. That…
Comment: Calculate RPKM by Chris ▴ 70
Thank you! How can I contact you?
Comment: Calculate RPKM by seidel 11k
You're welcome to contact me, but you should just ask the forum overall with a new question. You'll likely get much better answers.
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