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1,000 results • Page
1 of 20
Sort: replies
Rank
Views
Votes
Replies
41
votes
55
replies
8.8k
views
6 follow
hash function for DNA sequences
hash
hashing
DNA
6.2 years ago by
midox
▴ 290
4
votes
45
replies
5.5k
views
SAM file wrong? help with validatesamfile
EXOME
Tutorial
updated 5.8 years ago by
Biostar
20 • written 6.0 years ago by
cristina_sabiers
▴ 100
19
votes
43
replies
3.5k
views
Annotation of huge number of CNV files
CNV annotation TCGA
3.9 years ago by
nazaninhoseinkhan
▴ 430
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
17
votes
37
replies
2.6k
views
No alias or index file found for protein database
next-gen
software error
sequence
updated 3.1 years ago by
Biostar
20 • written 3.2 years ago by
williamsbrian5064
▴ 430
3
votes
32
replies
1.8k
views
fastqc report for degradome reads
fastqc
adaptor
4.2 years ago by
Sam
▴ 140
4
votes
30
replies
998
views
SNPs and DEL/MNP in the same position. (DEL or SNP ??)
snp
indels
vcf
calls
mpileup
updated 23 months ago by
Ram
36k • written 23 months ago by
sami
▴ 30
14
votes
30
replies
2.0k
views
Download GTF/GFF annotation data for NT database, not by organism (for STAR alignment)
RNA-Seq
rna-seq
alignment
next-gen
3.1 years ago by
Malka
▴ 70
4
votes
30
replies
854
views
Script makes different file then the manual command, but the command is the same
pipeline
linux
awk
24 months ago by
stan.aanhane
▴ 30
8
votes
30
replies
2.6k
views
Per Base Sequence Content
sequencing
fastqc
genome
sequence
updated 2.3 years ago by
wm
▴ 540 • written 2.3 years ago by
Negin
▴ 20
11
votes
29
replies
7.1k
views
SummarizedExperiment nrow differs from ncol
DESeq2
SummarizedExperiment
updated 8 months ago by
Ram
36k • written 8.0 years ago by
Parham
★ 1.6k
0
votes
29
replies
1.7k
views
concordance rate between SNP observed and SNP not observed
SNP
updated 4.0 years ago by
Biostar
20 • written 4.2 years ago by
nour.hadjz
▴ 20
7
votes
29
replies
1.2k
views
What's the powerful biological methods for significant genes selection?
gene selection
significant
biological method
R
3.6 years ago by
Chaimaa
▴ 260
12
votes
28
replies
1.5k
views
Calculating the expression level of genes
Gene expression
RNA-Seq
R
4.0 years ago by
Za
▴ 140
2
votes
28
replies
4.3k
views
Memory use in indexing
Assembly
software error
updated 3.9 years ago by
Ram
36k • written 4.1 years ago by
marongiu.luigi
▴ 650
9
votes
27
replies
5.1k
views
How do I use Glimmer 3.02?
sequencing
updated 3.4 years ago by
ojelizodun
• 0 • written 4.3 years ago by
nattzy94
▴ 50
4
votes
27
replies
3.0k
views
MISO test run fails error of bam file was not found
RNA-Seq
Assembly
software error
next-gen
genome
updated 18 months ago by
Biostar
20 • written 5.9 years ago by
JoeDoasi
▴ 10
3
votes
27
replies
4.0k
views
7 follow
Did anyone manage to successfully run HLAScan and get results?
HLA-Typing
NGS
updated 3.9 years ago by
Shiqi Li
• 0 • written 4.0 years ago by
zeynep
▴ 10
1
vote
26
replies
3.5k
views
plink --assoc command gives "NA" for all the analysis (F_A,F_U,A2,CHISQ,P,OR values)
SNP
plink
association
analysis
3.4 years ago by
kushagraprasad24
• 0
8
votes
25
replies
1.4k
views
construction of a database
neo4j
noSQL
sql
bioinformatic
database
updated 12 months ago by
Michael Dondrup
51k • written 13 months ago by
Debut
▴ 40
24
votes
25
replies
4.2k
views
How to generate Beta diversity boxplot from phyloseq object?
phyloseq
beta diversity
metagenomics
23 months ago by
dpc
▴ 240
10
votes
25
replies
2.2k
views
The interpretation of PCA
DESeq2
R
PCA
updated 3.9 years ago by
Biostar
20 • written 4.0 years ago by
Za
▴ 140
13
votes
24
replies
2.7k
views
Error of bam-to-sam conversion using samtools
samtools
TopHat2
RNA-Seq
BAM
SAM
updated 5.3 years ago by
GenoMax
117k • written 5.3 years ago by
Gary
▴ 480
5
votes
24
replies
5.7k
views
Plink1.9 gives error when converting VCF.gz to PED? "Error read failure"
VCF
Plink
4.0 years ago by
DanielC
▴ 150
11
votes
24
replies
3.3k
views
BWA mem skip orientation
assembly
genome
alignment
next-gen
3.2 years ago by
williamsbrian5064
▴ 430
0
votes
24
replies
1.9k
views
converting spaces to tabs in gtf files
NCBI
13 months ago by
storm1907
▴ 30
6
votes
23
replies
1.7k
views
Could you help me set up a VCF filter?
genome
software error
VCF filter
4.0 years ago by
Charlie2
▴ 50
1
vote
23
replies
725
views
Parse multifasta files based on a values in two columns in a metadata file
parse
mutlifasta
RefSeq
database
strain
22 months ago by
jmwhitha
• 0
1
vote
23
replies
724
views
FASTQ exctract ID's
fastq
2.5 years ago by
User000
▴ 550
10
votes
23
replies
1.5k
views
Two simillarly annotated sequence has no alignment similarity. Why?
blast
alignment
gene
updated 4.6 years ago by
GenoMax
117k • written 4.6 years ago by
Farbod
★ 3.3k
11
votes
22
replies
2.3k
views
No significant DEG: A request to double check my commands for limma.
limma
differential gene expression
covariates
3.2 years ago by
RNAseqer
▴ 200
5
votes
22
replies
2.1k
views
Differential analysis between two cell lines
R
RNA-Seq
edgeR
differential analysis
4.0 years ago by
Biologist
▴ 230
3
votes
22
replies
2.0k
views
Making RefSeq in Windows
refseq
5.9 years ago by
Alireza Ebadi Tabrizi
• 0
1
vote
22
replies
1.9k
views
Genome Index and Alignment- STAR
RNA-Seq
genome
alignment
STAR
updated 3.6 years ago by
Kevin Blighe
81k • written 3.6 years ago by
carolgalah
• 0
1
vote
22
replies
3.8k
views
how to use faSplit to split fasta into x files
next-gen
faSplit
sequence
3.6 years ago by
olechnwin
▴ 60
5
votes
22
replies
5.8k
views
SVM for classified gene expression data
R
svm
microarray
updated 6.4 years ago by
Biostar
20 • written 6.4 years ago by
Shaurya Jauhari
▴ 50
3
votes
22
replies
1.4k
views
samtools coverage usage
NGS
updated 12 months ago by
Lila M
★ 1.2k • written 12 months ago by
smrutimayipanda
▴ 20
13
votes
22
replies
8.0k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva
combat
batch effects
updated 4.8 years ago by
Biostar
20 • written 5.0 years ago by
lessismore
★ 1.2k
0
votes
22
replies
2.2k
views
Using java Treeview to analyse genes: how to select and compile group of genes to present?
RNA-Seq
4.2 years ago by
Muha0216
• 0
2
votes
21
replies
2.2k
views
Compute the correlations between submatrices
correlation
R
matrix
foreach
updated 3.2 years ago by
Ram
36k • written 3.2 years ago by
pablo
▴ 210
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
16
votes
21
replies
1.3k
views
Why there are different hit for a same gene in different species
gene
blast
ortholog
paralog
5.7 years ago by
Farbod
★ 3.3k
6
votes
21
replies
1.7k
views
How to evaluate the similarity of genes between two sample
RNA-Seq
differential
updated 3.8 years ago by
Biostar
20 • written 3.9 years ago by
afli
▴ 190
1
vote
21
replies
1.3k
views
Center and scale RIN values for DESeq2?
deseq2
rin
22 months ago by
randalljellis
▴ 90
10
votes
21
replies
1.8k
views
Calculate disease risk based on the genoytype of some SNPs?
SNP
prs
gwas
PRSice
Plink
updated 2.9 years ago by
Biostar
20 • written 2.9 years ago by
Miguel
▴ 10
3
votes
21
replies
2.1k
views
Normalization agilent microarray data?
Microarray
Normalization
updated 13 months ago by
Ram
36k • written 2.8 years ago by
mathavanbioinfo
▴ 60
7
votes
21
replies
2.0k
views
Merged.gtf vs. Rnor_6.0.gtf for Raw Counts
RNA-Seq
cuffmerge
raw counts
5.6 years ago by
jmsyl.hong
• 0
22
votes
20
replies
1.8k
views
what is the prefered strategy to treat with blast-less transcriptomes from RNA-seq
RNA-Seq
blast
gene
genome
Forum
5.9 years ago by
Farbod
★ 3.3k
6
votes
20
replies
4.8k
views
filling of missing genotype information in merged variant call vcf file
SNP
4.0 years ago by
princy149
▴ 80
9
votes
20
replies
2.7k
views
Solve SAM issues flagged by Picard's ValidateSamFile
Picard
SAM file
alignment error
3.9 years ago by
marongiu.luigi
▴ 650
1,000 results • Page
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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…
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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…
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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.
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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
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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
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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?
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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
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pifferdavide
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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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