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1,000 results • Page
3 of 20
Sort: Views
Rank
Views
Votes
Replies
6
votes
8
replies
10k
views
7 follow
Converting SNP names from Illumina GSA array to rsID using PLINK
SNP
plink
6.5 years ago by
dam4l
▴ 200
4
votes
6
replies
10.0k
views
Spades assembler output
Assembly
updated 21 months ago by
Ram
43k • written 8.3 years ago by
elbecerrasoto
▴ 30
0
votes
8
replies
9.9k
views
how to find a read by name in a bam file
next-gen-sequencing
updated 10 months ago by
Ram
43k • written 6.8 years ago by
himanimalhotra89
• 0
3
votes
10
replies
9.9k
views
How can I obtain SNP from TCGA?
Risky-allele
BRCA
SNP
updated 2.3 years ago by
Ram
43k • written 9.6 years ago by
purmod
▴ 10
3
votes
5
replies
9.9k
views
pheatmap: how to avoid fontface, fontsize, and color from writing over existing rownames
fontsize
rows
color
R
pheatmap
updated 3.0 years ago by
cpad0112
21k • written 3.0 years ago by
ladypurrsia
▴ 60
11
votes
29
replies
9.8k
views
SummarizedExperiment nrow differs from ncol
DESeq2
SummarizedExperiment
updated 2.5 years ago by
Ram
43k • written 9.9 years ago by
Parham
★ 1.6k
0
votes
2
replies
9.8k
views
DESeq2 pheatmap returns Error in check.length("fill") : 'gpar' element 'fill' must not be length 0
RNA-Seq
DESeq2
gpar
pheatmap
6.5 years ago by
Anthony.Knox
▴ 60
0
votes
4
replies
9.8k
views
How to install PLINK on linux/Mac-OS
genome
3.5 years ago by
giusdalt95
▴ 10
2
votes
2
replies
9.8k
views
Multiple whole genome alignment tools ?
multiple whole genome
alignment
4.9 years ago by
Picasa
▴ 640
4
votes
10
replies
9.7k
views
Questions about multithreading of BWA
bwa
multithread
updated 5.6 years ago by
Ram
43k • written 8.2 years ago by
michealsmith
▴ 790
1
vote
4
replies
9.7k
views
R ggplot Align Y-Axis on multiple graphs
ggarrange
ggplot2
r
updated 4.7 years ago by
Biostar
20 • written 6.2 years ago by
jjrin
▴ 40
1
vote
13
replies
9.7k
views
MDS Plot R
RNA-Seq
4.8 years ago by
BioBaby
▴ 20
2
votes
17
replies
9.7k
views
7 follow
EXITING: because of fatal INPUT file error: could not open read file
mapping
genome
fastq
STAR
updated 2.1 years ago by
todd.ugine
• 0 • written 3.3 years ago by
merfer0206
• 0
4
votes
3
replies
9.6k
views
Convert Tab delimited file to VCF file
snp
updated 23 months ago by
Ram
43k • written 8.5 years ago by
niharraul
• 0
1
vote
6
replies
9.6k
views
How to use python to process .CEL file?
cel
affymetrix
python
R
cmap
updated 23 months ago by
Ram
43k • written 9.1 years ago by
zero_hsy
▴ 110
5
votes
11
replies
9.6k
views
R- Kruskal-Wallis test on multiple columns at once
R
statistics
test
kruskal-Wallis
R-statistics
4.8 years ago by
mafernandez
• 0
0
votes
19
replies
9.6k
views
Skip orientation as there are not enough pairs by bwa mem
whole genome
bwa
paired end sequencing
4.9 years ago by
seta
★ 1.9k
3
votes
8
replies
9.5k
views
topTable in limma
limma
toptable
6.5 years ago by
AHW
▴ 90
3
votes
9
replies
9.5k
views
Random Forest returns "New factor levels not present in the training data"
R
Machine Learning
microarrays
6.2 years ago by
arronar
▴ 280
1
vote
6
replies
9.5k
views
Deseq2 : Filtering low counts before per sample
Deseq2
threshold-seq
5.5 years ago by
Cdk
• 0
3
votes
7
replies
9.5k
views
6 follow
remote blast requires installation of taxdb database
blast
updated 4.9 years ago by
Varshney
▴ 20 • written 6.6 years ago by
hfan22
▴ 40
3
votes
5
replies
9.5k
views
Using 'blastn' to do a remote search on NCBI BLAST against the nt collection database
blast
shell
unix
linux
6.2 years ago by
maciwuk
• 0
2
votes
2
replies
9.5k
views
Imputation Analysis In Plink?
plink
gwas
imputation
12.2 years ago by
Davy
▴ 210
7
votes
5
replies
9.5k
views
strange issues with absent EOF markers in BAM files
samtools
picard-tools
bam
eof
7.9 years ago by
abascalfederico
★ 1.2k
2
votes
12
replies
9.4k
views
8 follow
michigan imputation server
conversion
michigan imputation server
updated 2.4 years ago by
Fazil
• 0 • written 6.2 years ago by
Teresa
▴ 20
4
votes
2
replies
9.4k
views
Hisat2 versus Bowtie2
Exome-sequencing
hisat2
bowtie2
updated 6.8 years ago by
Biostar
20 • written 8.0 years ago by
nalpas.nicolas
▴ 20
2
votes
7
replies
9.4k
views
How to annotate TTS or TES
ChIP-Seq
TES
annotation
7.2 years ago by
Lila M
★ 1.2k
4
votes
8
replies
9.4k
views
Quantile normalizing prior to or after TPM scaling?
RNAseq
normalization
updated 14 months ago by
Kevin Blighe
87k • written 6.4 years ago by
mforde84
★ 1.4k
0
votes
11
replies
9.3k
views
Error in installation R package
R
updated 7.6 years ago by
Biostar
20 • written 7.7 years ago by
niutster
▴ 110
5
votes
12
replies
9.3k
views
ADMIXTURE: "Invalid chromosome code. Use integers!"
admixture
genome
7.2 years ago by
beneficii
▴ 60
7
votes
8
replies
9.3k
views
Removing rRNA and tRNA sequences using GTF files
RNA-Seq
7.7 years ago by
pixie@bioinfo
★ 1.5k
4
votes
1
reply
9.2k
views
Need help with heatmaps in R, how to draw select genes or selected pathway??
RNA-Seq
DESEQ2
R
heatmap
ontology
updated 7.6 years ago by
Biostar
20 • written 7.6 years ago by
marina.kimyr
▴ 20
3
votes
8
replies
9.2k
views
DiffBind: Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length
R
DiffBind
ChIP-Seq
5.1 years ago by
msimmer92
▴ 300
10
votes
11
replies
9.1k
views
How to adjust my manhattan plot to look better?
qqman
manhattan
R
updated 23 months ago by
Ram
43k • written 9.1 years ago by
SheelS
▴ 40
1
vote
2
replies
9.1k
views
Problem in merging 1000G and cases in Plink
merge
duplicate snp
plink
triallelic
1000G
7.6 years ago by
fatima
▴ 20
3
votes
10
replies
9.1k
views
How to remove outliers using PCA in R?
PCA
R
4.8 years ago by
zhaoliang0302
▴ 50
3
votes
4
replies
9.0k
views
how to filter vcf file based on sample DP? vcf tools does not work
vcf-filtering
sample DP
7.1 years ago by
Ana
▴ 200
3
votes
0
replies
9.0k
views
edgeR: how to make contrasts with makeContrasts
ngs
edgeR
makeContrasts
glm
dge
5.5 years ago by
m98
▴ 420
13
votes
13
replies
9.0k
views
How to do pca plot from .eigenval and .eigenvec files from Plink in R.
R
SNP
updated 6.1 years ago by
Devon Ryan
104k • written 6.1 years ago by
amitgourav.ghosh12
▴ 70
7
votes
8
replies
9.0k
views
Determining read count
trimmomatic
rna-seq
trinity
updated 8 months ago by
Ram
43k • written 8.0 years ago by
nikelle.petrillo
▴ 110
4
votes
9
replies
9.0k
views
bcftools consensus command
vcf
bcftools
updated 13 months ago by
Ram
43k • written 4.3 years ago by
Begonia_pavonina
▴ 150
3
votes
4
replies
8.9k
views
Design Pcr Primers To Uniquely Identify A Bacterial Strain
bacteria
pcr
updated 10.5 years ago by
Biostar
20 • written 10.6 years ago by
Eric Normandeau
11k
5
votes
10
replies
8.9k
views
GWAS - approximate odds ratio and standard error
GWAS
imputation
updated 6.6 years ago by
Kevin Blighe
87k • written 6.6 years ago by
alessandrotestori7
▴ 420
2
votes
3
replies
8.9k
views
what is the detailed information of .amb .ann .bwt .pac .sa files generated by the BWA aligner?
alignment
BWA
.ann
.bwt
.sa
updated 6.2 years ago by
WouterDeCoster
47k • written 6.2 years ago by
lffu_0032
▴ 90
2
votes
8
replies
8.8k
views
Questions: how to do GSEA for single cells?
RNA-Seq
3.9 years ago by
yingnanlei0202
▴ 20
1
vote
3
replies
8.8k
views
Htseq Count Finding No Feature
htseq
bacteria
gene-expression
11.1 years ago by
joaslucas
▴ 90
2
votes
2
replies
8.8k
views
Plot minor allele frequency distribution in R?
gwas
maf
R
8.0 years ago by
dam4l
▴ 200
0
votes
4
replies
8.8k
views
ITCN 1.6 ImageJ Plugin
software error
updated 6.5 years ago by
Biostar
20 • written 7.5 years ago by
verma
▴ 30
3
votes
13
replies
8.8k
views
Actually meaning of log2FoldChange, p-value & padj in DESeq2 results
RNA-Seq
DESeq2
differentially expressed genes
5.5 years ago by
hffqyd
▴ 10
1
vote
2
replies
8.8k
views
Install Plink V1.07 on Mac
software error
7.7 years ago by
xaviera417
• 0
1,000 results • Page
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Recent Votes
Comment: PDB related issue
Comment: PDB related issue
Comment: NGS forensics: how to know if data is fabricated
Comment: How many reads for WGS Sequencing?
Comment: How many reads for WGS Sequencing?
Comment: How many reads for WGS Sequencing?
Comment: How many reads for WGS Sequencing?
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Comment: Figures are disappeared from html report of SnpEff
by
analyst
▴ 30
Files are not opening in any of the computer (ubuntu/windows). I rereun snpEff annotation but still output html files are having missing im…
Comment: Figures are disappeared from html report of SnpEff
by
analyst
▴ 30
I reinstalled nodejs: > sudo apt-get install nodejs Its already up to date with version v10.19.0
Answer: NGS forensics: how to know if data is fabricated
by
Prash
▴ 270
Mensur, if I were you, I'd probably contact the CA directly and check with him whether they have reproduced the works recently. There coul…
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 550
Working on it - it's actually a bit difficult. Low coverage of ribosomal proteins. Low coverage of housekeeping genes ...I'm trying to find…
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 550
I'm a bit against pubpeer - have you ever posted there? My gripe with them is that the posts are heavily moderated and EDITED to the point…
Comment: NGS forensics: how to know if data is fabricated
by
Philipp Bayer
8.4k
Thanks Mensur! I'd add that in 9 out of 10 cases, you won't receive a reply to a request for raw data. That's just how scientists are, does…
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
I had downloaded the two files in a similar manner actually.
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
ok, i'll try to use fastp. I have only used trimmomatic and cutadapt till now and they dont identify on its own. Except the graph in fastqc…
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
got it! even if i'm doing the assembly for paired end with both the files do i have set the threshold to 1000bp ?
Comment: NGS forensics: how to know if data is fabricated
by
Philipp Bayer
8.4k
i've been in our org trying to push such a detector, our use-case is much more limited: I want to make simulated eDNA libraries as real as …
Answer: Differential Expression using Isoseq-supplemented reference transcriptome
by
Gordon Smyth
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> What is the best method to test for differential abundance at the isoform level? Salmon returns TPM values instead of the counts which Li…
Comment: NGS forensics: how to know if data is fabricated
by
benformatics
3.9k
Can you post an IGV screenshot of what this looks like?
Comment: NGS forensics: how to know if data is fabricated
by
benformatics
3.9k
Yeah some of the Illumina machines pre-trim adapters (not sure if this is still the standard). I've also definitely also seen quality-trimm…
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by
noodle
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You can typically find much more useful info in the cif file, for example what you've found is called '_atom_site.pdbx_PDB_ins_code ' and d…
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by
Mensur Dlakic
★ 27k
The best way to find out is to read the original paper. My guess is that the residue has been crystallized in alternative conformations, wh…
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