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1,000 results • Page 1 of 20
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23
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22
replies
38k
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 4 months ago by • 0 • written 4.9 years ago by ▴ 250
20
votes
15
replies
25k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink SNP
updated 8 months ago by 38k • written 7.2 years ago by ▴ 190
4
votes
13
replies
25k
views
6 follow
[main_samview] fail to read the header from sample.bam
alignment
updated 9 months ago by • 0 • written 5.1 years ago by ▴ 20
2
votes
8
replies
16k
views
Using vcfutils.pl command
alignment
updated 11 months ago by 38k • written 8.1 years ago by ▴ 40
16
votes
38
replies
15k
views
Differential gene Analysis by Limma
Limma Microarray R
updated 11 months ago by 38k • written 8.1 years ago by ▴ 920
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
2
votes
4
replies
14k
views
TRIMMOMATRIC Nextera trimming
next-gen
updated 5 months ago by 38k • written 7.7 years ago by ▴ 10
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
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
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
8
votes
5
replies
11k
views
samtools tview symbols
samtools
updated 4 months ago by 38k • written 7.7 years ago by ★ 1.4k
0
votes
4
replies
11k
views
Convert .gbf file to .gbk or .gff
gbk gff gbf
updated 10 weeks ago by 38k • written 7.9 years ago by • 0
2
votes
3
replies
10k
views
converting maf to vcf
Exome maf2vcf
updated 9 weeks ago by 38k • written 7.9 years ago by • 0
3
votes
1
reply
10k
views
Negative P-Values
gene genome next-gen-sequencing
updated 7 months ago by 38k • written 7.6 years ago by ▴ 200
0
votes
0
replies
9.2k
views
pheatmap row annotation and title font size questions
heatmap pheatmap
updated 11 weeks ago by 38k • written 7.9 years ago by • 0
3
votes
6
replies
9.2k
views
6 follow
How to calculate genetic correlation with R
R
updated 10 months ago by • 0 • written 8.9 years ago by ▴ 80
2
votes
8
replies
9.1k
views
Size of typical genomic data
genomic
updated 4 days ago by 38k • written 4.9 years ago by 10k
1
vote
6
replies
8.5k
views
How to use python to process .CEL file?
cel affymetrix python R cmap
updated 10 months ago by 38k • written 8.1 years ago by ▴ 110
4
votes
6
replies
8.4k
views
Spades assembler output
Assembly
updated 8 months ago by 38k • written 7.2 years ago by ▴ 30
4
votes
3
replies
8.4k
views
Convert Tab delimited file to VCF file
snp
updated 10 months ago by 38k • written 7.5 years ago by • 0
10
votes
11
replies
8.2k
views
How to adjust my manhattan plot to look better?
qqman manhattan R
updated 10 months ago by 38k • written 8.0 years ago by ▴ 40
18
votes
4
replies
8.1k
views
How To Find Rna-Seq Data Of Published Papers?
geo next-gen RNA-seq
updated 4 weeks ago by 38k • written 9.7 years ago by ▴ 930
3
votes
8
replies
8.1k
views
Quantile normalizing prior to or after TPM scaling?
RNAseq normalization
updated 6 weeks ago by 85k • written 5.3 years ago by ★ 1.4k
5
votes
4
replies
7.8k
views
GFF3 to GTF conversion - 9th column
gtf NCBI gff3 featureCounts
updated 8 months ago by 38k • written 7.2 years ago by ▴ 50
2
votes
7
replies
7.8k
views
linux 'cat' command merge fasta files without headers
fasta linux
updated 25 days ago by 38k • written 8.8 years ago by • 0
2
votes
2
replies
7.8k
views
How to filter out special sequences from a fasta file based on sequence IDs txt
fasta
updated 7 months ago by 38k • written 7.5 years ago by ▴ 130
1
vote
2
replies
7.6k
views
vcf compare between 2 vcf files using vcf tools
vcftools
updated 18 days ago by 38k • written 6.3 years ago by ▴ 220
2
votes
1
reply
7.5k
views
ROH by PLINK
plink ROH
updated 7 weeks ago by 38k • written 7.9 years ago by ▴ 20
1
vote
2
replies
7.2k
views
Converting vcf to fasta format
fasta samtools vcf alignment next-gen
updated 3 months ago by 38k • written 7.8 years ago by ▴ 10
3
votes
7
replies
7.2k
views
RNA-STAR, mapping problem (number of reads)
RNA-Seq
updated 8 months ago by 38k • written 7.1 years ago by • 0
4
votes
2
replies
7.0k
views
PLINK Merge error: File write failure
plink 1000genomes
updated 7 months ago by 38k • written 7.5 years ago by ▴ 70
1
vote
6
replies
6.8k
views
using bcftools/samtools to generate consensus using reference + variants; output is a truncated reference
samtools bcftools mosaik consensus rc454
updated 10 months ago by 38k • written 8.0 years ago by ▴ 10
2
votes
7
replies
6.7k
views
Bowtie2 run out of memory
software-error alignment bowtie2
updated 8 weeks ago by 38k • written 7.9 years ago by ▴ 50
4
votes
9
replies
6.7k
views
bcftools consensus command
vcf bcftools
updated 9 days ago by 38k • written 3.2 years ago by ▴ 90
0
votes
0
replies
6.7k
views
Error in grid.Call.graphics(L_setviewport, vp, TRUE) : non-finite location and/or size for viewport
gviz
updated 8 months ago by 38k • written 7.6 years ago by • 0
0
votes
10
replies
6.7k
views
Error: reads file does not look like a fastq file
fastq bowtie2 ChIP-Seq
updated 14 days ago by 38k • written 6.5 years ago by ▴ 40
3
votes
5
replies
6.6k
views
Visualising the number of overlapping peaks in ChIP-seq studies
ChIP-Seq
updated 8 months ago by 38k • written 7.1 years ago by ★ 3.4k
2
votes
5
replies
6.5k
views
Tophat Protocol Error Occured At Step 4
tophat rna-seq
updated 10 months ago by 38k • written 10.8 years ago by ▴ 100
0
votes
2
replies
6.5k
views
Illumina adapter diagram
illumina sequencing adapter-trimming
updated 9 months ago by 38k • written 8.0 years ago by • 0
5
votes
22
replies
6.4k
views
SVM for classified gene expression data
R svm microarray
updated 8 months ago by 38k • written 7.2 years ago by ▴ 50
3
votes
5
replies
6.3k
views
Converting Vcftools output to R readable format
vcf SNP R vcftools
updated 9 weeks ago by 38k • written 7.9 years ago by ▴ 100
10
votes
5
replies
6.3k
views
how to remove asterisk characters from a translated sequences (fasta format)?
sequencing Assembly alignment
updated 7 months ago by 38k • written 7.6 years ago by ★ 1.8k
4
votes
8
replies
6.3k
views
Error while demultipleaxing .bcl to .fastq files
sequencing genome alignment
updated 6 months ago by 38k • written 7.5 years ago by ▴ 220
5
votes
11
replies
6.3k
views
Error while running miso
RNA-Seq splicing
updated 8 months ago by 38k • written 7.6 years ago by ▴ 40
0
votes
0
replies
6.3k
views
E-values calculation (MEME)
meme
updated 10 weeks ago by 38k • written 7.9 years ago by ▴ 10
0
votes
3
replies
6.3k
views
Cross validation error Admixture
SNP software-error
updated 10 months ago by 38k • written 8.1 years ago by • 0
1
vote
8
replies
6.1k
views
Plotting different gene ontology categories in a barplot
HI Gene ontology R
updated 8 months ago by 11k • written 2.1 years ago by • 0
3
votes
2
replies
6.0k
views
Hypergeometric test of gene set enrichment - Calculate P-value for multiple gene sets in one script?
next-gen R GO
updated 11 months ago by 38k • written 8.2 years ago by ▴ 20
2
votes
1
reply
6.0k
views
BEDgraph to BED/bam
bed
updated 5 months ago by 38k • written 7.6 years ago by ▴ 60
1,000 results • Page 1 of 20
Recent Votes
Comment: My keys are all ENSEMBL, but R says they are not valid keys for ENSEMBL
Answer: How to remove duplicate reads after ONT basecalling from fastq.gz files
Talk from Aaron Lun on Orchestrating Single-Cell Analysis With Bioconductor
SSPACE for scaffolding
Answer: Snakemake workflow for trimmomatic
Answer: How to remove duplicate reads after ONT basecalling from fastq.gz files
A: Why Chip-seq data cross correlation plot has fragment_lenth cross correlation p
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Recent Replies
Comment: pyCirclize - Circular visualization in Python by moshi ▴ 90
Please install Biopython with v1.80 or higher. If biopython>=1.80, there should be no errors.
Comment: Gene family classification using RNA-seq data by Dion • 0
well, I have been given the task to retrieve gene family/categorization. I found sveral papers on family classification, but no actual pack…
Comment: pyCirclize - Circular visualization in Python by karenkvn ▴ 40
Thank you for this wonderful programme! I am plotting a bacterial chromosome and find that when I plot the NC_000913 chromosome using the e…
Comment: SKAT in R by Eliza ▴ 20
@acvill can you sujjest maybe pther tools , methods for this ? ( also for every SNP i have data how many patients had the hetro/homozygous…
Comment: TCGA-BRCA tissue and RNAseq problem by pinheirofabiano ▴ 10
Go to https://portal.gdc.cancer.gov > Exploration > select TCGA and the cancer type you want > select case ID to download the files and hav…
Answer: Snakemake workflow for trimmomatic by antoine.fauchois92 • 0
Thank you very much for your reply ! It's working now !
Comment: Dependent p values by Eliza ▴ 20
@lchart I'm sorry for asking another of questions but I'm new to this field , can you please explain a little more how to use SKAT , saige…
Comment: How to deal with the probe id mapping to multiple gene ids? by dare_devil ★ 1.7k
similar question [here][1], [here][2] and [here][3] [1]: https://support.bioconductor.org/p/54838/ [2]: https://support.bioconductor.…
Comment: How to deal with the probe id mapping to multiple gene ids? by dare_devil ★ 1.7k
@genomax I have used the same platform file only. If you look at probe id and their corresponding `Gene Symbol` or `ENTREZ_GENE_ID` you can…
Comment: How to deal with the probe id mapping to multiple gene ids? by GenoMax 127k
Where are you seeing this? [Platform file for this array][1] on GEO has these names uniquely assigned. [1]: https://www.ncbi.nlm.nih.go…
Comment: My keys are all ENSEMBL, but R says they are not valid keys for ENSEMBL by rpolicastro 11k
`Org.Mm.eg.db` is the mouse organism database, but your ENSEMBL IDs are for human genes. Mouse ensembl ids start with `ENSMUSG`. You proba…
Comment: Snakemake doesn't recognize output files even though they are created by DdogBoss • 0
Yes, it completed the dry run. What other information do you need?
Comment: LDSC correlation calculate confidence intervals by YL ▴ 10
Based on my personal thought, I think the se from LDSC output probably needs to be transferred using Delta method based on Fisher transform…
Comment: LDSC correlation calculate confidence intervals by YL ▴ 10
Hi, Are you able to find an answer for this? I have the exact question! YL
Answer: Gene duplicate by ATpoint 71k
Use use ensembID_geneName as gene identifier to avoid that. These duplicate names exist as genes so removing them is somewhat not really da…
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