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1,000 results • Page
1 of 20
Sort: Views
Rank
Views
Votes
Replies
23
votes
22
replies
40k
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 5 months ago by
Nicole
• 0 • written 5.1 years ago by
gaelgarcia
▴ 250
4
votes
13
replies
26k
views
6 follow
[main_samview] fail to read the header from sample.bam
alignment
updated 10 months ago by
Qboy
• 0 • written 5.2 years ago by
sambioinfo2018
▴ 20
20
votes
15
replies
26k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink
SNP
updated 10 months ago by
Ram
39k • written 7.4 years ago by
dam4l
▴ 190
0
votes
3
replies
14k
views
How to choose a TPM cut-off point
RNA-Seq
transcript
tpm
updated 9 months ago by
Ram
39k • written 7.6 years ago by
amyfm
▴ 10
2
votes
4
replies
14k
views
TRIMMOMATRIC Nextera trimming
next-gen
updated 7 months ago by
Ram
39k • written 7.8 years ago by
meekadi
▴ 10
0
votes
4
replies
12k
views
Unable to install XLconnect package in R studio version 3.2.1
R
updated 7 months ago by
Ram
39k • written 7.8 years ago by
Debbie
▴ 10
2
votes
4
replies
12k
views
Run BLAST on Linux terminal
ncbi
nBLAST
linux
blast
updated 8 months ago by
Ram
39k • written 7.6 years ago by
Abdul Rafay Khan
★ 1.2k
8
votes
5
replies
11k
views
samtools tview symbols
samtools
updated 6 months ago by
Ram
39k • written 7.9 years ago by
biolab
★ 1.4k
0
votes
4
replies
11k
views
Convert .gbf file to .gbk or .gff
gbk
gff
gbf
updated 4 months ago by
Ram
39k • written 8.0 years ago by
che.bellaj
• 0
2
votes
3
replies
11k
views
converting maf to vcf
Exome
maf2vcf
updated 4 months ago by
Ram
39k • written 8.0 years ago by
ashishchahl
• 0
3
votes
1
reply
10k
views
Negative P-Values
gene
genome
next-gen-sequencing
updated 9 months ago by
Ram
39k • written 7.7 years ago by
stevenlang123
▴ 200
1
vote
8
replies
9.9k
views
How to update rlang in R?
rlang
R
7 months ago by
Amr
▴ 140
0
votes
0
replies
9.4k
views
pheatmap row annotation and title font size questions
heatmap
pheatmap
updated 4 months ago by
Ram
39k • written 8.0 years ago by
neokao
• 0
2
votes
8
replies
9.3k
views
Size of typical genomic data
genomic
updated 8 weeks ago by
Ram
39k • written 5.0 years ago by
Nicolas Rosewick
10k
4
votes
6
replies
8.7k
views
Spades assembler output
Assembly
updated 10 months ago by
Ram
39k • written 7.4 years ago by
elbecerrasoto
▴ 30
4
votes
3
replies
8.6k
views
Convert Tab delimited file to VCF file
snp
updated 12 months ago by
Ram
39k • written 7.6 years ago by
niharraul
• 0
10
votes
11
replies
8.3k
views
How to adjust my manhattan plot to look better?
qqman
manhattan
R
updated 12 months ago by
Ram
39k • written 8.2 years ago by
SheelS
▴ 40
3
votes
8
replies
8.3k
views
Quantile normalizing prior to or after TPM scaling?
RNAseq
normalization
updated 3 months ago by
Kevin Blighe
85k • written 5.5 years ago by
mforde84
★ 1.4k
18
votes
4
replies
8.2k
views
How To Find Rna-Seq Data Of Published Papers?
geo
next-gen
RNA-seq
updated 3 months ago by
Ram
39k • written 9.8 years ago by
user
▴ 930
5
votes
4
replies
7.9k
views
GFF3 to GTF conversion - 9th column
gtf
NCBI
gff3
featureCounts
updated 10 months ago by
Ram
39k • written 7.4 years ago by
mrodrigues.fernanda
▴ 50
2
votes
7
replies
7.9k
views
linux 'cat' command merge fasta files without headers
fasta
linux
updated 11 weeks ago by
Ram
39k • written 8.9 years ago by
esterbuiate
• 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 9 months ago by
Ram
39k • written 7.6 years ago by
Ginsea Chen
▴ 130
1
vote
2
replies
7.8k
views
vcf compare between 2 vcf files using vcf tools
vcftools
updated 10 weeks ago by
Ram
39k • written 6.5 years ago by
bioguy24
▴ 230
2
votes
1
reply
7.6k
views
ROH by PLINK
plink
ROH
updated 3 months ago by
Ram
39k • written 8.1 years ago by
afadda
▴ 20
3
votes
7
replies
7.3k
views
RNA-STAR, mapping problem (number of reads)
RNA-Seq
updated 10 months ago by
Ram
39k • written 7.3 years ago by
mohikran
• 0
1
vote
2
replies
7.3k
views
Converting vcf to fasta format
fasta
samtools
vcf
alignment
next-gen
updated 5 months ago by
Ram
39k • written 7.9 years ago by
JW
▴ 10
4
votes
2
replies
7.2k
views
PLINK Merge error: File write failure
plink
1000genomes
updated 9 months ago by
Ram
39k • written 7.6 years ago by
aritra90
▴ 70
4
votes
9
replies
7.1k
views
bcftools consensus command
vcf
bcftools
updated 9 weeks ago by
Ram
39k • written 3.3 years ago by
Begonia_pavonina
▴ 100
1
vote
8
replies
6.9k
views
Plotting different gene ontology categories in a barplot
HI
Gene ontology
R
updated 10 months ago by
zx8754
11k • written 2.3 years ago by
aradhana
• 0
0
votes
10
replies
6.9k
views
Error: reads file does not look like a fastq file
fastq
bowtie2
ChIP-Seq
updated 10 weeks ago by
Ram
39k • written 6.7 years ago by
addilynn.beach
▴ 40
2
votes
7
replies
6.9k
views
Bowtie2 run out of memory
software-error
alignment
bowtie2
updated 3 months ago by
Ram
39k • written 8.0 years ago by
anon
▴ 50
3
votes
5
replies
6.8k
views
Visualising the number of overlapping peaks in ChIP-seq studies
ChIP-Seq
updated 10 months ago by
Ram
39k • written 7.3 years ago by
James Ashmore
★ 3.4k
0
votes
0
replies
6.8k
views
Error in grid.Call.graphics(L_setviewport, vp, TRUE) : non-finite location and/or size for viewport
gviz
updated 10 months ago by
Ram
39k • written 7.7 years ago by
nasim.zeeshan25
• 0
5
votes
22
replies
6.6k
views
SVM for classified gene expression data
R
svm
microarray
updated 10 months ago by
Ram
39k • written 7.4 years ago by
Shaurya Jauhari
▴ 50
0
votes
2
replies
6.5k
views
Illumina adapter diagram
illumina
sequencing
adapter-trimming
updated 11 months ago by
Ram
39k • written 8.1 years ago by
pjkriebel
• 0
4
votes
11
replies
6.5k
views
Correct way to calculate VAF (Variant allele fraction) from a VCF file
VCF
snp
9 months ago by
prasundutta87
▴ 650
10
votes
5
replies
6.4k
views
how to remove asterisk characters from a translated sequences (fasta format)?
sequencing
Assembly
alignment
updated 9 months ago by
Ram
39k • written 7.7 years ago by
seta
★ 1.8k
4
votes
8
replies
6.4k
views
Error while demultipleaxing .bcl to .fastq files
sequencing
genome
alignment
updated 8 months ago by
Ram
39k • written 7.7 years ago by
ravi.uhdnis
▴ 220
5
votes
11
replies
6.4k
views
Error while running miso
RNA-Seq
splicing
updated 10 months ago by
Ram
39k • written 7.8 years ago by
priyankamaripuri
▴ 40
3
votes
5
replies
6.4k
views
Converting Vcftools output to R readable format
vcf
SNP
R
vcftools
updated 4 months ago by
Ram
39k • written 8.0 years ago by
pifferdavide
▴ 100
0
votes
0
replies
6.3k
views
E-values calculation (MEME)
meme
updated 4 months ago by
Ram
39k • written 8.0 years ago by
anahochmanova
▴ 10
4
votes
45
replies
6.3k
views
SAM file wrong? help with validatesamfile
EXOME
updated 7 weeks ago by
Ram
39k • written 6.9 years ago by
cristina_sabiers
▴ 110
2
votes
10
replies
6.2k
views
fq.gz file use
BioEdit
R
updated 10 weeks ago by
Ram
39k • written 4.2 years ago by
choi.yisoo.hi
• 0
2
votes
1
reply
6.1k
views
BEDgraph to BED/bam
bed
updated 7 months ago by
Ram
39k • written 7.8 years ago by
wanziyi89
▴ 60
8
votes
2
replies
6.1k
views
Differential gene expression analysis in Python
python
R
updated 3 months ago by
Ram
39k • written 19 months ago by
Leendert
▴ 30
1
vote
7
replies
6.0k
views
Panther pathway Database
gene
updated 10 months ago by
Ram
39k • written 7.3 years ago by
nvayin
• 0
4
votes
3
replies
6.0k
views
PLINK2 association study using covariate regression model
SNP
plink
software-error
genome
updated 12 months ago by
Ram
39k • written 8.2 years ago by
tracylee7001
▴ 20
3
votes
1
reply
6.0k
views
how is the output of bcftools stats calculated?
bcftools
updated 8 months ago by
Ram
39k • written 7.8 years ago by
james.blackshaw
▴ 20
6
votes
13
replies
6.0k
views
DESeq2 and edgeR - no agreement between results
RNA-Seq
edgeR
DESeq2
updated 9 months ago by
Ram
39k • written 7.5 years ago by
ilyco
▴ 60
1
vote
6
replies
6.0k
views
bedGRAPH files from MACS2 ChIP-seq analysis don't reflect peaks called in peak.xls file
ChIP-Seq
updated 8 months ago by
Ram
39k • written 7.7 years ago by
nash.claire
▴ 470
1,000 results • Page
1 of 20
Recent Votes
A: how to count variants par sample per chromosome in a vcf file?
Comment: DEgs RNAseq
Answer: ScRNA data
Answer: extract all fasta sequence from db v5
Does the RNAseq data normal if the TPM value 3rd Qutile expression is near 10, but the Max expression are near 20,000
Comment: Does the RNAseq data normal if the TPM value 3rd Qutile expression is near 10, b
Answer: Does the RNAseq data normal if the TPM value 3rd Qutile expression is near 10, b
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Recent Replies
Comment: Error in download library file in expression console software
by
GenoMax
129k
What software is this referring to?
Comment: Single cell chemistry
by
GenoMax
129k
As you can see the data is one base short. If cell ranger is unable to analyze the data you may need to look elsewhere.
Comment: Bioinformatics Master's Student
by
Mensur Dlakic
★ 23k
`Bioinformatics Master's Student` is not an informative title for your question. I imagine most people will ignore it by assuming that this…
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by
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> what coordinate sorting is exactly? https://www.biostars.org/p/319730/#319750 > Why coordinate-sort is required coordinate sort is de …
Comment: Bioinformatics Master's Student
by
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why the read is like this ?? I know I should contains (ATGC) not (T2200330123010111..03100022.....023..02.....011022.)
Answer: Bioinformatics Master's Student
by
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It's a fastq file. So what is the question?
Comment: Single cell chemistry
by
swbarnes2
13k
As far as I know, v2 must mean 10x. But if it the cell barcode + umi is 26 bases, you don't have that.
Comment: best annotation approach for peaks
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Hi, I don't understand why, if I change TSS +1000/-1000 or +3000/-3000 or +10.000/-10.000 the number of regions annotated is the same. More…
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Thank you, I will check it out
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I actually have replicates. thank you
Comment: Why are some WES VCFs larger than others?
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Jeremy Leipzig
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"It's not a gvcf with site coverage for the entire cohort, I called the variants myself" This sentence doesn't make sense to me. gVCFs are …
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It seems the data appears to be in the beta value format (?), which represents the proportion of methylated probe intensity over the total …
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Hi, can you please add the link to the page you mentioned? AFAIK some data have restricted access. Maybe full GWAS data belongs to this cat…
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Did you come across this? https://www.biostars.org/p/432297/ Regards, Prasun
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David
• 0
Unlikely, this data came from a experienced sequencing team, I 'm the inexperienced data analyst. I'm not sure if these samples are 10x, …
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