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1,000 results • Page
1 of 20
Sort: Views
Rank
Views
Votes
Replies
23
votes
22
replies
50k
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 17 months ago by
Nicole
• 0 • written 6.0 years ago by
gaelgarcia
▴ 270
4
votes
4
replies
42k
views
How to convert a URL into a DOI programmatically
pubmed
doi
url
written 7.7 years ago by
entheologist33
▴ 100
4
votes
13
replies
35k
views
6 follow
[main_samview] fail to read the header from sample.bam
alignment
updated 22 months ago by
Qboy
▴ 10 • written 6.2 years ago by
sambioinfo2018
▴ 20
20
votes
15
replies
30k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink
SNP
updated 21 months ago by
Ram
43k • written 8.4 years ago by
dam4l
▴ 200
5
votes
6
replies
29k
views
terminate called after throwing an instance of 'std::bad_alloc?
bedtools
linux
data
5.1 years ago by
star
▴ 350
2
votes
3
replies
29k
views
How to extract vcf.gz and vcf.gz.tbi
SNP
sequence
gene
updated 5.9 years ago by
Pierre Lindenbaum
161k • written 5.9 years ago by
elhlalisoufiane
▴ 30
3
votes
4
replies
23k
views
Using nr database for BLAST search
nr
database
blast
blastp
updated 7.7 years ago by
Biostar
20 • written 7.8 years ago by
cookm346
▴ 20
13
votes
4
replies
23k
views
What is the definition of "read depth" vs "coverage"? (again...)
coverage
depth
read depth
7.0 years ago by
ariel.balter
▴ 260
28
votes
17
replies
22k
views
12 follow
Dotplot for filtered pathways result
pathways
ggplot2
clusterProfiler
r
dotplot
2.5 years ago by
Leite
★ 1.3k
3
votes
3
replies
22k
views
Subsetting - Raw Counts from Seurat Object
seurat
raw counts
RNA-Seq
4.1 years ago by
David_emir
▴ 490
2
votes
4
replies
21k
views
Error in file(file, "rt") : cannot open the connection
R
MicroRNA TXT FORMAT
updated 8.1 years ago by
GenoMax
142k • written 8.1 years ago by
31sharmajittu1991
• 0
7
votes
16
replies
21k
views
featureCounts: Low percentage of assigned fragments
RNA-Seq
rna-seq
7.8 years ago by
aggregatibacter
▴ 180
1
vote
5
replies
20k
views
Calculating the sequence similarity and percentage of matched sequences
alignment
sequence
updated 6.5 years ago by
eteleeb
• 0 • written 6.5 years ago by
ago1mutant
▴ 10
2
votes
8
replies
18k
views
Using vcfutils.pl command
alignment
updated 2.1 years ago by
Ram
43k • written 9.3 years ago by
lcc1844
▴ 40
2
votes
10
replies
18k
views
How do you use the Aspera ascp command?
aspera
gigascience
gigaDb
updated 2.7 years ago by
Ram
43k • written 8.6 years ago by
cyril-cros
▴ 950
13
votes
13
replies
18k
views
How to interpret Per sequence GC content module in FastQC for RNA-seq data?
RNA-Seq
FastQC
QC
GC-content
4.8 years ago by
Arindam Ghosh
▴ 510
16
votes
38
replies
17k
views
Differential gene Analysis by Limma
Limma
Microarray
R
updated 2.1 years ago by
Ram
43k • written 9.3 years ago by
Mo
▴ 920
16
votes
14
replies
17k
views
Which truseq trimmomatic adapters file to use when removing truseq adapters?
adapters
trimmomatic
RNA-seq
5.9 years ago by
salamandra
▴ 550
4
votes
18
replies
17k
views
Alignment with BWA and SAMtools
BWA
SAM-file
SAMtools
updated 3.5 years ago by
Biostar
20 • written 5.8 years ago by
Shelle
▴ 30
2
votes
13
replies
17k
views
convert text file to fasta file
blast
updated 7.7 years ago by
GouthamAtla
12k • written 7.7 years ago by
sukesh1411
▴ 30
1
vote
8
replies
17k
views
How to update rlang in R?
rlang
R
19 months ago by
Amr
▴ 160
1
vote
5
replies
17k
views
pheatmap: how to use legend information as row annotation?
R
pheatmap
legend
annotation
6.1 years ago by
n85825
• 0
5
votes
4
replies
16k
views
glmnet package lasso error
glmnet
lasso
multilinear regression
6.2 years ago by
demoraesdiogo2017
▴ 100
0
votes
3
replies
16k
views
How to choose a TPM cut-off point
RNA-Seq
transcript
tpm
updated 21 months ago by
Ram
43k • written 8.6 years ago by
amyfm
▴ 10
6
votes
2
replies
16k
views
Pacbio Ccs Vs Subreads Explained ?
updated 10.1 years ago by
Biostar
20 • written 10.6 years ago by
curious.genome
▴ 40
0
votes
8
replies
16k
views
find ORF in sequence python
sequence
updated 7.4 years ago by
natasha.sernova
★ 4.0k • written 7.4 years ago by
elisheva
▴ 120
3
votes
8
replies
16k
views
Error when running pheatmap
pheatmap
Error in hclust
5.1 years ago by
luzglongoria
▴ 50
2
votes
4
replies
16k
views
TRIMMOMATRIC Nextera trimming
next-gen
updated 19 months ago by
Ram
43k • written 8.8 years ago by
meekadi
▴ 10
4
votes
10
replies
16k
views
How to plot a multiple line graph with Mean and Std Error for following dataset?
R
updated 6.1 years ago by
GenoMax
142k • written 6.1 years ago by
WUSCHEL
▴ 760
2
votes
2
replies
15k
views
How to calculate the insert size for Paired-end reads
SSPACE
insert-size
7.9 years ago by
Ric
▴ 430
9
votes
13
replies
15k
views
Sort bam file by coordinates using samtools
next-gen-sequencing
gene
rna-seq
updated 11 months ago by
Ram
43k • written 5.7 years ago by
Shahzad
▴ 30
8
votes
4
replies
15k
views
Use of if-else statement in snakemake rule
snakemake
if-else
python
updated 4.5 years ago by
schroder.julia
• 0 • written 6.9 years ago by
Jokhe
▴ 140
0
votes
3
replies
15k
views
How to change/remove name of annotation ComplexHeatmap package?
ComplexHeatmap
R
RNA-Seq
annotations
updated 3.9 years ago by
Ram
43k • written 3.9 years ago by
camillab.
▴ 160
4
votes
1
reply
15k
views
Converting BigBed to Bed format
Installing BigFile Support
8.9 years ago by
sumaira.zaman10
▴ 20
1
vote
13
replies
15k
views
"[E::bgzf_read] Read block operation failed" error - possible truncation/corruption of BAM file
samtools
updated 3.0 years ago by
darklings
▴ 570 • written 4.6 years ago by
gordo2b
• 0
1
vote
8
replies
15k
views
HTSeq-count high number of no_feature
htseq-count
rna-seq
updated 2.1 years ago by
Ram
43k • written 9.3 years ago by
cafelumiere12
▴ 80
6
votes
13
replies
15k
views
Fastq file is truncated error message
RNA-Seq
error
fastq
8.0 years ago by
rob.costa1234
▴ 310
4
votes
1
reply
15k
views
How do you normalize Transcript per Million TPM to compare between samples ?
RNA-Seq
TPM
STAR
salmon
quantification
7.3 years ago by
ZheFrench
▴ 580
9
votes
13
replies
15k
views
GC Content of Fasta file --- Python Help
sequence
7.2 years ago by
Patrick Brennan
▴ 50
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
10.0 years ago by
ira_grich
• 0
0
votes
2
replies
14k
views
Error in -delete: invalid argument to unary operator
RNA-Seq
R
4.2 years ago by
ovariohisterectomia
▴ 40
6
votes
13
replies
14k
views
Showing FDR and log2FC in Volcano plot using R
R
RNA-Seq
volcano plot
updated 5.0 years ago by
zx8754
11k • written 6.5 years ago by
Farbod
★ 3.4k
8
votes
5
replies
14k
views
The comparison between HISAT2 and Tophat2
RNA-Seq
Tophat2
HISAT2
updated 5.7 years ago by
Ram
43k • written 8.3 years ago by
Peng Huang
▴ 50
4
votes
12
replies
14k
views
STAR alignment error- Segmentation fault (core dumped)
alignment
software error
RNA-Seq
STAR
5.9 years ago by
EagleEye
7.5k
2
votes
1
reply
13k
views
Rename Idents in Seurat Object
RNA-Seq
4.0 years ago by
Thorerges
▴ 10
0
votes
2
replies
13k
views
How to download pfam database
sequence
updated 7.3 years ago by
Medhat
9.7k • written 7.3 years ago by
Sanchita Gupta
▴ 30
3
votes
11
replies
13k
views
What is the acceptable % of reads that map to no feature (in RNASeq)?
htseq
RNA-Seq
STAR
updated 2.1 years ago by
Ram
43k • written 9.3 years ago by
noushin.farnoud
▴ 130
0
votes
2
replies
13k
views
GSEA error - After pruning, none of the gene sets passed size thresholds
RNA-Seq
GSEA
gene
genome
updated 4.8 years ago by
Morris_Chair
▴ 360 • written 4.8 years ago by
limjustinj
• 0
0
votes
3
replies
13k
views
edgeR: likelihood ratio test or quasi-likelihood F-test?
R
rna-seq
next-gen
7.1 years ago by
moxu
▴ 510
0
votes
4
replies
13k
views
Unable to install XLconnect package in R studio version 3.2.1
R
updated 19 months ago by
Ram
43k • written 8.8 years ago by
Debbie
▴ 10
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Recent Replies
Comment: DRAGEN gVCF files and joint calling GATK-GenomicsDB
by
DBScan
▴ 300
I think I did it once, but why would you use GATK with DRAGEN gVCF files? If you have a DRAGEN, the iterative gVCF Genotyper does a much fa…
Answer: Practical Haplotype Graph v2 not finding correct paths
by
beantkapoor16
▴ 10
So, I just tested it and it's performing much better now. Most of the haplotype paths are coming from the expected haplotypes (australasica…
Comment: Kraken2 Custom Database non-deterministic results
by
Bjorn
• 0
Thank you!
Comment: Generating a Bed file from a Fasta file
by
Pierre Lindenbaum
161k
there is not enough information. you have to show us the command you used, a snapshot of your fasta...
Comment: Practical Haplotype Graph v2 not finding correct paths
by
beantkapoor16
▴ 10
That's great. I will test it and let you know how it goes. Thank you.
Comment: Generating a Bed file from a Fasta file
by
pirku
• 0
I tried running BLAT, but the output looks like this. Seems like none of the sequences were mapped/aligned match mis- rep. N's Q gap…
Comment: Where to find old version of GATK best practice
by
GenoMax
142k
You could try and look up a snapshot of the page(s) - https://web.archive.org/ Which specific best practice are you referring to? https:/…
Comment: Generating a Bed file from a Fasta file
by
Pierre Lindenbaum
161k
you could run blast or any other aligner to get the coordinate(s) of your fasta on a reference genome.
Answer: Running STRUCTURE from command line
by
Arthur
• 0
If it cans help, I got the same error message : There were errors in the input file (listed above). According to "mainparams" the inp…
Comment: CreateSeuratObject taking very long
by
Nitin Narwade
★ 1.6k
I am not sure whether it will speedup the conversion but you can give it a try. convert your dataframe into a sparse matrix before creatin…
Comment: Practical Haplotype Graph v2 not finding correct paths
by
pjb39
▴ 220
The timing for your question is excellent. The fix was released yesterday.
Comment: vcf phasing
by
WouterDeCoster
47k
> I observed that it doesn't phase genotypes labeled as 0/0 How could such a genotype even be phased?
Comment: Super ehancers
by
Oburah
• 0
Well-noted however just wondering what you me by GFF being shorter. Thank you![See the screeshot snap of the gff file][1] [1]: /media/i…
Comment: What marks a De-Novo Genome assembly as FAILED?
by
Umer
▴ 50
I know illumina will only give me high-quality contigs. the samples which are to be sequenced with Long_Short read sequence will be used as…
Comment: What marks a De-Novo Genome assembly as FAILED?
by
Umer
▴ 50
Hi, Thank you for a detailed responce. Let me add some more informations. Long-Read is ~75X coverage. Short-Read is ~100X coverage. **For…
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