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1,000 results • Page 1 of 20
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23
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22
replies
36k
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 9 weeks ago by • 0 • written 4.7 years ago by ▴ 250
19
votes
15
replies
25k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink SNP
updated 6 months ago by 37k • written 7.1 years ago by ▴ 180
4
votes
13
replies
23k
views
6 follow
[main_samview] fail to read the header from sample.bam
alignment
updated 7 months ago by • 0 • written 4.9 years ago by ▴ 20
2
votes
8
replies
16k
views
Using vcfutils.pl command
alignment
updated 9 months ago by 37k • written 8.0 years ago by ▴ 40
16
votes
38
replies
15k
views
Differential gene Analysis by Limma
Limma Microarray R
updated 9 months ago by 37k • written 8.0 years ago by ▴ 920
0
votes
3
replies
14k
views
How to choose a TPM cut-off point
RNA-Seq transcript tpm
updated 5 months ago by 37k • written 7.3 years ago by ▴ 10
2
votes
4
replies
13k
views
TRIMMOMATRIC Nextera trimming
next-gen
updated 3 months ago by 37k • written 7.5 years ago by ▴ 10
1
vote
8
replies
13k
views
HTSeq-count high number of no_feature
htseq-count rna-seq
updated 9 months ago by 37k • written 8.0 years ago by ▴ 80
0
votes
4
replies
12k
views
Unable to install XLconnect package in R studio version 3.2.1
R
updated 4 months ago by 37k • written 7.5 years ago by ▴ 10
2
votes
4
replies
12k
views
Run BLAST on Linux terminal
ncbi nBLAST linux blast
updated 5 months ago by 37k • written 7.3 years ago by ★ 1.2k
3
votes
11
replies
12k
views
What is the acceptable % of reads that map to no feature (in RNASeq)?
htseq RNA-Seq STAR
updated 9 months ago by 37k • written 8.0 years ago by ▴ 120
8
votes
5
replies
11k
views
samtools tview symbols
samtools
updated 3 months ago by 37k • written 7.5 years ago by ★ 1.4k
0
votes
4
replies
10k
views
Convert .gbf file to .gbk or .gff
gbk gff gbf
updated 15 days ago by 37k • written 7.7 years ago by • 0
2
votes
3
replies
10k
views
converting maf to vcf
Exome maf2vcf
updated 11 days ago by 37k • written 7.7 years ago by • 0
3
votes
1
reply
10k
views
Negative P-Values
gene genome next-gen-sequencing
updated 5 months ago by 37k • written 7.4 years ago by ▴ 200
2
votes
0
replies
9.9k
views
How to plot UniFrac PCoA with 95% confidence Elipses in R
metagenomics ordiellipse vegan R phyloseq
updated 10 months ago by 37k • written 8.1 years ago by ▴ 100
0
votes
0
replies
9.1k
views
pheatmap row annotation and title font size questions
heatmap pheatmap
updated 24 days ago by 37k • written 7.7 years ago by • 0
3
votes
6
replies
9.0k
views
6 follow
How to calculate genetic correlation with R
R
updated 8 months ago by • 0 • written 8.8 years ago by ▴ 80
1
vote
6
replies
8.3k
views
How to use python to process .CEL file?
cel affymetrix python R cmap
updated 8 months ago by 37k • written 7.9 years ago by ▴ 110
4
votes
6
replies
8.2k
views
Spades assembler output
Assembly
updated 6 months ago by 37k • written 7.1 years ago by ▴ 30
10
votes
11
replies
8.1k
views
How to adjust my manhattan plot to look better?
qqman manhattan R
updated 8 months ago by 37k • written 7.9 years ago by ▴ 40
4
votes
3
replies
8.0k
views
Convert Tab delimited file to VCF file
snp
updated 8 months ago by 37k • written 7.3 years ago by • 0
2
votes
2
replies
7.7k
views
How to filter out special sequences from a fasta file based on sequence IDs txt
fasta
updated 5 months ago by 37k • written 7.3 years ago by ▴ 130
5
votes
4
replies
7.6k
views
GFF3 to GTF conversion - 9th column
gtf NCBI gff3 featureCounts
updated 6 months ago by 37k • written 7.0 years ago by ▴ 50
7
votes
18
replies
7.5k
views
9 follow
Cuffmerge running error
RNA-Seq
updated 11 months ago by 37k • written 8.2 years ago by ▴ 190
1
vote
2
replies
7.2k
views
Converting vcf to fasta format
fasta samtools vcf alignment next-gen
updated 7 weeks ago by 37k • written 7.6 years ago by ▴ 10
3
votes
7
replies
7.1k
views
RNA-STAR, mapping problem (number of reads)
RNA-Seq
updated 6 months ago by 37k • written 7.0 years ago by • 0
0
votes
4
replies
6.8k
views
Problem With Autodock 4.2.5
docking
updated 10 months ago by 37k • written 10.1 years ago by ▴ 70
4
votes
2
replies
6.8k
views
PLINK Merge error: File write failure
plink 1000genomes
updated 5 months ago by 37k • written 7.3 years ago by ▴ 70
1
vote
6
replies
6.7k
views
using bcftools/samtools to generate consensus using reference + variants; output is a truncated reference
samtools bcftools mosaik consensus rc454
updated 8 months ago by 37k • written 7.9 years ago by ▴ 10
4
votes
7
replies
6.6k
views
How to create chain file to change genome coordinates from one genome version to another
remap liftover chain-format
updated 11 months ago by 37k • written 8.3 years ago by 5.7k
0
votes
0
replies
6.6k
views
Error in grid.Call.graphics(L_setviewport, vp, TRUE) : non-finite location and/or size for viewport
gviz
updated 6 months ago by 37k • written 7.4 years ago by • 0
2
votes
7
replies
6.6k
views
Bowtie2 run out of memory
software-error alignment bowtie2
updated 13 hours ago by 37k • written 7.7 years ago by ▴ 50
6
votes
3
replies
6.5k
views
How to set a threshold for coefficient of variation in RNA-seq?
dispersion statistics single-cell RNA-Seq variance
updated 10 months ago by 37k • written 8.0 years ago by ▴ 250
0
votes
2
replies
6.5k
views
High light specific dot in scatterplot
R
updated 11 months ago by 37k • written 8.2 years ago by ▴ 170
3
votes
5
replies
6.5k
views
Visualising the number of overlapping peaks in ChIP-seq studies
ChIP-Seq
updated 6 months ago by 37k • written 7.0 years ago by ★ 3.4k
2
votes
5
replies
6.5k
views
Tophat Protocol Error Occured At Step 4
tophat rna-seq
updated 8 months ago by 37k • written 10.7 years ago by ▴ 100
0
votes
2
replies
6.5k
views
Illumina adapter diagram
illumina sequencing adapter-trimming
updated 7 months ago by 37k • written 7.8 years ago by • 0
5
votes
22
replies
6.3k
views
SVM for classified gene expression data
R svm microarray
updated 6 months ago by 37k • written 7.1 years ago by ▴ 50
2
votes
1
reply
6.3k
views
Difference between UPGMA and the NJ
UPGMA phylogenetics NJ
updated 11 months ago by 37k • written 8.2 years ago by ▴ 10
3
votes
5
replies
6.2k
views
Converting Vcftools output to R readable format
vcf SNP R vcftools
updated 11 days ago by 37k • written 7.7 years ago by ▴ 100
0
votes
0
replies
6.2k
views
E-values calculation (MEME)
meme
updated 15 days ago by 37k • written 7.7 years ago by ▴ 10
5
votes
11
replies
6.2k
views
Error while running miso
RNA-Seq splicing
updated 6 months ago by 37k • written 7.5 years ago by ▴ 40
0
votes
3
replies
6.2k
views
Cross validation error Admixture
SNP software-error
updated 8 months ago by 37k • written 7.9 years ago by • 0
4
votes
8
replies
6.1k
views
Error while demultipleaxing .bcl to .fastq files
sequencing genome alignment
updated 4 months ago by 37k • written 7.4 years ago by ▴ 220
10
votes
5
replies
6.1k
views
how to remove asterisk characters from a translated sequences (fasta format)?
sequencing Assembly alignment
updated 5 months ago by 37k • written 7.4 years ago by ★ 1.7k
2
votes
3
replies
6.1k
views
bwa mem failed to allocate memory
bwa-mem bwa
updated 10 months ago by 37k • written 8.0 years ago by ▴ 90
2
votes
1
reply
6.0k
views
FANTOM5 TSS downloads by cell line
fantom5 cell-lines
updated 11 months ago by 37k • written 8.2 years ago by ▴ 60
1
vote
7
replies
5.9k
views
Panther pathway Database
gene
updated 6 months ago by 37k • written 7.0 years ago by • 0
3
votes
2
replies
5.9k
views
Hypergeometric test of gene set enrichment - Calculate P-value for multiple gene sets in one script?
next-gen R GO
updated 10 months ago by 37k • written 8.0 years ago by ▴ 20
1,000 results • Page 1 of 20
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Recent Replies
Comment: Diffbind losing peaks when going from small to larger consensus peak set by tara.mcintyre • 0
I'm now realizing it might be due to the filter parameter being set =1 when I run dba.count because when I set it to 0, all of the peaks ar…
Answer: Obtaining every"Protein ID" from a genome in OMA by clement.train ▴ 40
Hello, It seems that the current download is limited to 100 genes on the genomes pages, we will increase this limit to the extent of ea…
Comment: DNA methylation (RRBS/WGBS) prediction from DNA sequence (WGS) by Lalaland ▴ 10
Thank you very much, Matthias! I will definitely check those links out myself!
Comment: RNA Editing data from RNA-seq by Juke34 7.5k
What tool did you look at ?
Comment: want the codes for Deseq2 to perform DEGs. by rupali • 0
thanks for help
Comment: cellranger-arc mkfastq Error: bcl2fastq was killed with signal -11 by Yingying • 0
Hi, Yes I've uploaded the diagnostic file to 10x support already, but haven't got any response yet.
Comment: cellranger-arc mkfastq Error: bcl2fastq was killed with signal -11 by GenoMax 125k
You may want to contact 10x tech support. When this process failed it must have created a diagnostic archive. You also get a message about …
Answer: How to merge unique/non overlapping genes between 2 gene model GFF3 files? by jv ▴ 780
`bedtools intersect -v` is one option for identifying the unique genes from the older gene model. <https://bedtools.readthedocs.io/en/lates…
Comment: Alien-hunter outputs by schlogl ▴ 130
@GenoMax Hope this helps...Thank you
Comment: DESeq2 results function runs very slow on Windows 10 by ATpoint 68k
Does it go away if you remove the `parallel` from `results()`? After all, it is the `DESeq()` function that is the bottleneck when n is lar…
Comment: HTSeq error processing GFF file by ibq.enriquepola • 0
enrique@L:~/bioinformatica/index/prueba$ head -n 997531 GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_genomic.gff|tail -n 1 NC_007982.1 Ref…
Comment: Which file and data structure is used to create volcano plot from scRNA-Seq expe by Chris ▴ 60
Thank you for your help! I got an error that I could not find the solution on the Internet: library(EnhancedVolcano) Loading required…
Comment: HTSeq error processing GFF file by barslmn ★ 1.2k
I guess you can try to replace the "?" to a "." Also, you can copy and paste text instead of the screenshots?
Answer: DESeq2 results function runs very slow on Windows 10 by Istvan Albert 96k
Note the following: https://support.bioconductor.org/p/115415/ it looks like it has to do with the Parallel=TRUE flag
Comment: DESeq2 results function runs very slow on Windows 10 by GenoMax 125k
> there is a massive difference in performance between them. It still is taking only one minute.
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