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1,000 results • Page
1 of 20
Sort: Views
Rank
Views
Votes
Replies
23
votes
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 3 months ago by
Nicole
• 0 • written 4.9 years ago by
gaelgarcia
▴ 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
entheologist33
▴ 100
20
votes
15
replies
25k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink
SNP
updated 7 months ago by
Ram
38k • written 7.2 years ago by
dam4l
▴ 190
4
votes
13
replies
25k
views
6 follow
[main_samview] fail to read the header from sample.bam
alignment
updated 8 months ago by
Qboy
• 0 • written 5.1 years ago by
sambioinfo2018
▴ 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
Pierre Lindenbaum
153k • written 4.7 years ago by
elhlalisoufiane
▴ 20
3
votes
4
replies
21k
views
Using nr database for BLAST search
nr
database
blast
blastp
updated 6.6 years ago by
Biostar
20 • written 6.7 years ago by
cookm346
▴ 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 7.0 years ago by
GenoMax
127k • written 7.0 years ago by
31sharmajittu1991
• 0
1
vote
5
replies
17k
views
Calculating the sequence similarity and percentage of matched sequences
alignment
sequence
updated 5.3 years ago by
eteleeb
• 0 • written 5.4 years ago by
ago1mutant
▴ 10
7
votes
16
replies
17k
views
featureCounts: Low percentage of assigned fragments
RNA-Seq
rna-seq
6.7 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
Ram
38k • written 8.1 years ago by
lcc1844
▴ 40
2
votes
10
replies
16k
views
How do you use the Aspera ascp command?
aspera
gigascience
gigaDb
updated 18 months ago by
Ram
38k • written 7.5 years ago by
cyril-cros
▴ 940
16
votes
38
replies
15k
views
Differential gene Analysis by Limma
Limma
Microarray
R
updated 11 months ago by
Ram
38k • written 8.1 years ago by
Mo
▴ 920
2
votes
13
replies
15k
views
convert text file to fasta file
blast
updated 6.6 years ago by
GouthamAtla
12k • written 6.6 years ago by
sukesh1411
▴ 30
6
votes
2
replies
15k
views
Pacbio Ccs Vs Subreads Explained ?
updated 8.9 years ago by
Biostar
20 • written 9.4 years ago by
curious.genome
▴ 40
0
votes
8
replies
15k
views
find ORF in sequence python
sequence
updated 6.2 years ago by
natasha.sernova
★ 3.9k • written 6.2 years ago by
elisheva
▴ 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
15k
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
GenoMax
127k • written 4.9 years ago by
WUSCHEL
▴ 720
0
votes
3
replies
14k
views
How to choose a TPM cut-off point
RNA-Seq
transcript
tpm
updated 7 months ago by
Ram
38k • written 7.4 years ago by
amyfm
▴ 10
16
votes
14
replies
14k
views
Which truseq trimmomatic adapters file to use when removing truseq adapters?
adapters
trimmomatic
RNA-seq
4.8 years ago by
salamandra
▴ 530
5
votes
4
replies
14k
views
glmnet package lasso error
glmnet
lasso
multilinear regression
5.1 years ago by
demoraesdiogo2017
▴ 90
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
Ram
38k • written 7.7 years ago by
meekadi
▴ 10
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
Ram
38k • written 8.1 years ago by
cafelumiere12
▴ 80
8
votes
5
replies
13k
views
The comparison between HISAT2 and Tophat2
RNA-Seq
Tophat2
HISAT2
updated 4.6 years ago by
Ram
38k • written 7.1 years ago by
Peng Huang
▴ 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 3.4 years ago by
schroder.julia
• 0 • written 5.7 years ago by
Jokhe
▴ 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
5.0 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
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
zx8754
11k • written 5.3 years ago by
Farbod
★ 3.4k
0
votes
2
replies
12k
views
How to download pfam database
sequence
updated 6.2 years ago by
Medhat
9.5k • written 6.2 years ago by
Sanchita Gupta
▴ 30
0
votes
4
replies
12k
views
Unable to install XLconnect package in R studio version 3.2.1
R
updated 5 months ago by
Ram
38k • written 7.6 years ago by
Debbie
▴ 10
4
votes
1
reply
12k
views
Converting BigBed to Bed format
Installing BigFile Support
7.8 years ago by
sumaira.zaman10
▴ 20
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
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
Ram
38k • written 8.2 years ago by
noushin.farnoud
▴ 120
2
votes
4
replies
12k
views
Run BLAST on Linux terminal
ncbi
nBLAST
linux
blast
updated 6 months ago by
Ram
38k • written 7.5 years ago by
Abdul Rafay Khan
★ 1.2k
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
finswimmer
16k • written 4.5 years ago by
Shahzad
▴ 30
4
votes
18
replies
12k
views
Alignment with BWA and SAMtools
BWA
SAM-file
SAMtools
updated 2.4 years ago by
Biostar
20 • written 4.6 years ago by
Shelle
▴ 30
1
vote
2
replies
12k
views
kart file in prefetch
rna-seq
updated 6.4 years ago by
Biostar
20 • written 6.6 years ago by
zh.khodadadi
▴ 20
0
votes
1
reply
11k
views
PLINK 1.9 - Converting PED/MAP to BED/BIM/FAM with missing values
plink
updated 6.7 years ago by
Biostar
20 • written 6.7 years ago by
rednalf
▴ 80
0
votes
3
replies
11k
views
Extracting Specific Columns from Multiple Files & Writing to File Python
python
file-handeling
6.9 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 3.7 years ago by
Morris_Chair
▴ 330 • written 3.7 years ago by
limjustinj
• 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
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Recent Votes
Answer: Scaling RNA-Seq data before clustering?
Answer: How to use CAFE from Orthofinder Results
Answer: merge vcf.gz file
STAR solo set parameters for scrna-seq
STAR solo set parameters for scrna-seq
Sites for Computer Aided Drug Designing
Comment: mpileup to sync file
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Comment: merge vcf.gz file
by
Mali
• 0
file1 = '/sci/labs/orzuk/orzuk/projects/Skin/data/Ichilov/vcfFiles/vcfFiles/eb3_1001_748-gatk-haplotype.final.vcf.gz' file2 = '/sci/labs/or…
Comment: Which GPU for local Colabfold
by
matt_arnold_bio
• 0
Another giveaway is that when you hit run, it will say either "Running on GPU" or "Running on CPU" in the log output... ![enter image desc…
Answer: Which GPU for local Colabfold
by
matt_arnold_bio
• 0
Hi Arjen, This is a little while ago now so maybe this is not that helpful but... You should be able to tell if the GPU is being seen…
Comment: STAR solo set parameters for scrna-seq
by
t.ru
▴ 20
it's single cell mars-seq. Yes sorry its a fastq file.
Answer: boxplot issue
by
yura.grabovska
▴ 50
First of all, you're not outputting the result of your scale to anything... t(apply(mat, 1, scale)) colnames(mat) <- rownames(cold…
Comment: STAR solo set parameters for scrna-seq
by
GenoMax
127k
> a fasta file similar to this This is not a fasta file It is a fastq format file. Are you sure this is single cell RNAseq data? Looking…
Answer: heatmap issue
by
yura.grabovska
▴ 50
Your controls clearly show variable expression for the genes you're plotting so to get them to stick together on the left, you would need t…
Comment: How to demultiplex single end - dual index run - NextSeq 500
by
GenoMax
127k
Correct. This is a single-end dual indexed (8 bp each) run.
Comment: genome annotation [sstart] [send] - how to get protein sequence from gene
by
danfarkas
• 0
Hi shenwei356, Thanks for the clarification. However, I did try this, and it was not yielding the expected amino acid sequences. This is w…
Comment: Artificial reads - remove multiple mapped reads against reference genome, and on
by
Agamemnon
▴ 60
I ran ```samtools view -F 4 -q 42 test.bam | wc -l``` and I get ```6159141```, why is there a discrepancy, as originally only ```5200484```…
Comment: differential gene analysis
by
kalyani
• 0
okay thankks!
Comment: Kallisto bustools for scRNA-seq
by
t.ru
▴ 20
@SRR17050039.1 NB501465:544:HF2H7BGXB:1:22104:14442:1233_TCCTGAGC_barcode=NA-EEEE-AAAAAEE-EEEEEEEE-GCTG-TGCCAGA-ACGTTCAT-W202012/1 GCCCTGTA…
Comment: merge vcf.gz file
by
Pierre Lindenbaum
153k
"file 1 " , with a space, cannot be a real argument. show us the real filenames please, and the error messages.
Answer: merge vcf.gz file
by
ATpoint
70k
You must compress with bgzip. gzip -d your.vcf.gz bgzip your.vcf
Comment: GO enrichment analysis
by
hellokwmin
• 0
Thank you for your reply. Unfortunately, the organism I am using is non-model organism (i.e. one of plant species). So, with the informati…
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