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1,000 results • Page
1 of 20
Sort: Views
Rank
Views
Votes
Replies
23
votes
21
replies
30k
views
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
4.1 years ago by
gaelgarcia
▴ 250
4
votes
4
replies
28k
views
How to convert a URL into a DOI programmatically
pubmed
doi
url
written 5.7 years ago by
entheologist33
▴ 100
15
votes
14
replies
22k
views
6 follow
Converting SNP from chr:pos to rs number using PLINK?
SNP
plink
updated 6.3 years ago by
Biostar
20 • written 6.5 years ago by
dam4l
▴ 180
4
votes
6
replies
19k
views
terminate called after throwing an instance of 'std::bad_alloc?
bedtools
linux
data
3.2 years ago by
star
▴ 290
3
votes
4
replies
19k
views
Using nr database for BLAST search
nr
database
blast
blastp
updated 5.8 years ago by
Biostar
20 • written 5.9 years ago by
cookm346
▴ 20
1
vote
3
replies
19k
views
How to extract vcf.gz and vcf.gz.tbi
SNP
sequence
gene
updated 4.0 years ago by
Pierre Lindenbaum
146k • written 4.0 years ago by
elhlalisoufiane
▴ 20
2
votes
4
replies
19k
views
Error in file(file, "rt") : cannot open the connection
R
MicroRNA TXT FORMAT
updated 6.2 years ago by
GenoMax
117k • written 6.2 years ago by
31sharmajittu1991
• 0
9
votes
4
replies
18k
views
What is the definition of "read depth" vs "coverage"? (again...)
coverage
depth
read depth
5.1 years ago by
ariel.balter
▴ 190
4
votes
12
replies
17k
views
[main_samview] fail to read the header from sample.bam
alignment
updated 11 months ago by
ATpoint
62k • written 4.3 years ago by
sambioinfo2018
▴ 20
0
votes
5
replies
16k
views
Calculating the sequence similarity and percentage of matched sequences
alignment
sequence
updated 4.6 years ago by
eteleeb
• 0 • written 4.6 years ago by
ago1mutant
• 0
7
votes
16
replies
15k
views
featureCounts: Low percentage of assigned fragments
RNA-Seq
rna-seq
5.9 years ago by
aggregatibacter
▴ 170
2
votes
8
replies
15k
views
Using vcfutils.pl command
alignment
updated 9 weeks ago by
Ram
36k • written 7.4 years ago by
lcc1844
▴ 40
16
votes
38
replies
15k
views
Differential gene Analysis by Limma
Limma
Microarray
R
updated 8 weeks ago by
Ram
36k • written 7.4 years ago by
Mo
▴ 920
6
votes
2
replies
14k
views
Pacbio Ccs Vs Subreads Explained ?
updated 8.2 years ago by
Biostar
20 • written 8.7 years ago by
curious.genome
▴ 40
2
votes
10
replies
14k
views
How do you use the Aspera ascp command?
aspera
gigascience
gigaDb
updated 9 months ago by
Ram
36k • written 6.7 years ago by
cyril-cros
▴ 920
0
votes
8
replies
14k
views
find ORF in sequence python
sequence
updated 5.5 years ago by
natasha.sernova
★ 3.9k • written 5.5 years ago by
elisheva
▴ 110
2
votes
13
replies
14k
views
convert text file to fasta file
blast
updated 5.8 years ago by
GouthamAtla
12k • written 5.8 years ago by
sukesh1411
▴ 30
2
votes
2
replies
14k
views
How to calculate the insert size for Paired-end reads
SSPACE
insert-size
6.0 years ago by
Ric
▴ 400
4
votes
10
replies
13k
views
How to plot a multiple line graph with Mean and Std Error for following dataset?
R
updated 4.2 years ago by
GenoMax
117k • written 4.2 years ago by
WUSCHEL
▴ 560
27
votes
17
replies
13k
views
12 follow
Dotplot for filtered pathways result
pathways
ggplot2
clusterProfiler
r
dotplot
6 months ago by
Leite
★ 1.2k
0
votes
3
replies
13k
views
Error in (function (classes, fdef, mtable): unable to find an inherited method for function ‘annotation’ for signature ‘"character
inSilicoMerging
8.1 years ago by
ira_grich
• 0
3
votes
1
reply
13k
views
How do you normalize Transcript per Million TPM to compare between samples ?
RNA-Seq
TPM
STAR
salmon
quantification
5.4 years ago by
ZheFrench
▴ 460
8
votes
5
replies
13k
views
The comparison between HISAT2 and Tophat2
RNA-Seq
Tophat2
HISAT2
updated 3.8 years ago by
Ram
36k • written 6.4 years ago by
Peng Huang
▴ 50
0
votes
3
replies
12k
views
How to choose a TPM cut-off point
tpm
RNA-Seq
transcript
6.7 years ago by
amyfm
▴ 10
2
votes
4
replies
12k
views
TRIMMOMATRIC Nextera trimming
next-gen
updated 6.8 years ago by
Biostar
20 • written 6.9 years ago by
meekadi
▴ 10
1
vote
8
replies
12k
views
HTSeq-count high number of no_feature
htseq-count
rna-seq
updated 9 weeks ago by
Ram
36k • written 7.4 years ago by
cafelumiere12
▴ 80
4
votes
4
replies
12k
views
glmnet package lasso error
glmnet
lasso
multilinear regression
4.3 years ago by
demoraesdiogo2017
▴ 60
9
votes
13
replies
12k
views
GC Content of Fasta file --- Python Help
sequence
5.3 years ago by
Patrick Brennan
▴ 50
16
votes
14
replies
12k
views
Which truseq trimmomatic adapters file to use when removing truseq adapters?
adapters
trimmomatic
RNA-seq
4.0 years ago by
salamandra
▴ 460
2
votes
4
replies
12k
views
Run BLAST on Linux terminal
linux
nBLAST
blast
ncbi
6.7 years ago by
Abdul Rafay Khan
★ 1.2k
0
votes
4
replies
12k
views
Unable to install XLconnect package in R studio version 3.2.1
R
updated 2.9 years ago by
sansritisinha
• 0 • written 6.9 years ago by
Debbie
▴ 10
6
votes
13
replies
11k
views
Showing FDR and log2FC in Volcano plot using R
R
RNA-Seq
volcano plot
updated 3.1 years ago by
zx8754
11k • written 4.6 years ago by
Farbod
★ 3.3k
0
votes
2
replies
11k
views
How to download pfam database
sequence
updated 5.4 years ago by
Medhat
9.3k • written 5.4 years ago by
Sanchita Gupta
▴ 30
7
votes
4
replies
11k
views
Use of if-else statement in snakemake rule
snakemake
if-else
python
updated 2.6 years ago by
schroder.julia
• 0 • written 5.0 years ago by
Jokhe
▴ 120
3
votes
11
replies
11k
views
What is the acceptable % of reads that map to no feature (in RNASeq)?
htseq
RNA-Seq
STAR
updated 10 weeks ago by
Ram
36k • written 7.4 years ago by
noushin.farnoud
▴ 120
0
votes
3
replies
11k
views
Extracting Specific Columns from Multiple Files & Writing to File Python
python
file-handeling
6.1 years ago by
BioICoder
▴ 40
0
votes
1
reply
11k
views
PLINK 1.9 - Converting PED/MAP to BED/BIM/FAM with missing values
plink
updated 5.9 years ago by
Biostar
20 • written 5.9 years ago by
rednalf
▴ 70
6
votes
13
replies
11k
views
Fastq file is truncated error message
RNA-Seq
error
fastq
6.1 years ago by
rob.costa1234
▴ 310
4
votes
1
reply
11k
views
Converting BigBed to Bed format
Installing BigFile Support
7.0 years ago by
sumaira.zaman10
▴ 20
1
vote
2
replies
11k
views
kart file in prefetch
rna-seq
updated 5.6 years ago by
Biostar
20 • written 5.8 years ago by
zh.khodadadi
▴ 20
1
vote
5
replies
11k
views
pheatmap: how to use legend information as row annotation?
R
pheatmap
legend
annotation
4.2 years ago by
n85825
• 0
2
votes
3
replies
10k
views
Subsetting - Raw Counts from Seurat Object
seurat
raw counts
RNA-Seq
2.2 years ago by
David_emir
▴ 430
3
votes
4
replies
10k
views
Zlib.Error: -3 While Decompressing: Invalid Distance To Far Back (By Using Macs For Chip-Seq Data)
error
10.8 years ago by
Lisanne
• 0
3
votes
8
replies
10k
views
Error when running pheatmap
pheatmap
Error in hclust
3.2 years ago by
luzglongoria
▴ 40
4
votes
7
replies
10k
views
Grab Coordinate Of Centromeres From Ucsc
ucsc
9.1 years ago by
jeansimon32
▴ 160
3
votes
2
replies
10k
views
ExAC PLI score calculation
DNA-Seq
5.3 years ago by
jonessara770
▴ 230
3
votes
1
reply
10k
views
Negative P-Values ????
genome
next-gen
gene
sequencing
6.8 years ago by
stevenlang123
▴ 200
8
votes
5
replies
10k
views
samtools tview symbols
samtools
tview
6.9 years ago by
biolab
★ 1.4k
7
votes
9
replies
9.9k
views
Different alignment rates for Hisat2 and STAR, Hisat2 has lower alignment rate and STAR have many multi aligned reads
RNA-Seq
updated 4.8 years ago by
Satyajeet Khare
★ 1.6k • written 4.8 years ago by
SMILE
▴ 170
0
votes
2
replies
9.9k
views
Error in -delete: invalid argument to unary operator
RNA-Seq
R
2.3 years ago by
ovariohisterectomia
▴ 20
1,000 results • Page
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Recent Replies
Comment: Computing allele frequencies per individual for a set of SNPs in PLINK
by
chrchang523
9.3k
If 1kgtot.bim contains doubled IDs (e.g. "HG00096 HG00096", you need to provide a doubled ID to `--indv`. The log file shows that your scr…
Answer: ESTIMATE tumor purity
by
JACKY
▴ 10
Just in case anyone faces this problem in the future, here is the link for the updated `estimate package` on github: https://github.com/…
Answer: Exctract unmapped reads from BLAST
by
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117k
> Is there a way to tell blast to output the unmapped reads into a > separate file? No there is not. You will need to use `-outfmt 7` whe…
Comment: Resfams Database usage
by
Neel
▴ 10
Hi, i have annotated genome by prokka and o want to search amr agaisnt resfams could you please tell me how to do it steps by steps.
Comment: Exctract unmapped reads from BLAST
by
Pierre Lindenbaum
146k
those are two distinct commands https://linux.die.net/man/1/comm and https://linux.die.net/man/1/join extract the names of your queries, s…
Comment: Exctract unmapped reads from BLAST
by
Pilar
• 0
Thanks for answering :), sorry, I'm new at this. These are commands I should use when I launch Blast in terminal?
Comment: Exctract unmapped reads from BLAST
by
Pierre Lindenbaum
146k
have a look at `comm` or `join`.
Comment: Computing allele frequencies per individual for a set of SNPs in PLINK
by
pifferdavide
▴ 100
Sorry I forgot to mention I used it in this loop, which worked with another plink file, but not with this 1KG file. for popfile in $(l…
Comment: Computing allele frequencies per individual for a set of SNPs in PLINK
by
chrchang523
9.3k
`--indv` takes a single ID, not a filename. So `--indv IDlist.txt` shouldn't work.
Answer: Quast Ouput
by
Ying
• 0
The "# contigs 47484" is based on contig of size >= 500 bp (see the first line of your screenshot). The "# contigs (>= 0 bp)" is the raw nu…
Answer: SRA obtained metagenomic reads appears to corrupt - cannot work on SingleM
by
Mensur Dlakic
★ 19k
Not sure why: 1) you are splitting reads; 2) you are fixing reads when they seem fine. I suggest something like this instead after `prefetc…
Comment: Quick way to get a field such as QNAME from the last read in a bam file?
by
kalavattam
▴ 70
Thank you. Do you know of any strategies for non-coordinated-sorted bam files?
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@rpolicastro gave you several helpful links for using the h5ad file, in addition to how to explore and plot data. The links in my answer al…
Comment: Computing allele frequencies per individual for a set of SNPs in PLINK
by
pifferdavide
▴ 100
I was able to run the --indv command successfully on a file with a bed file by simply listing the IDs in single column. However, with anoth…
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tomas4482
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1. design a RNA-seq experiment specifically seuqencing non-coding RNA/circRNA sequencing. 2. subset to interested region -> extract chi…
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