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1,000 results • Page
1 of 20
Sort: replies
Rank
Views
Votes
Replies
41
votes
55
replies
12k
views
6 follow
hash function for DNA sequences
hash
hashing
DNA
8.0 years ago by
midox
▴ 290
4
votes
45
replies
7.5k
views
SAM file wrong? help with validatesamfile
EXOME
updated 11 months ago by
Ram
43k • written 7.8 years ago by
cristina_sabiers
▴ 110
19
votes
43
replies
5.5k
views
Annotation of huge number of CNV files
CNV annotation TCGA
5.6 years ago by
nazaninhoseinkhan
▴ 520
16
votes
38
replies
17k
views
Differential gene Analysis by Limma
Limma
Microarray
R
updated 23 months ago by
Ram
43k • written 9.1 years ago by
Mo
▴ 920
17
votes
37
replies
4.6k
views
No alias or index file found for protein database
next-gen
software error
sequence
updated 4.8 years ago by
Biostar
20 • written 5.0 years ago by
williamsbrian5064
▴ 510
5
votes
35
replies
3.5k
views
Reduce set of chromosomes in Pangenome graph
pangenome
vg
updated 8 months ago by
Jordan M Eizenga
▴ 460 • written 9 months ago by
anivlete
• 0
3
votes
32
replies
3.3k
views
fastqc report for degradome reads
fastqc
adaptor
6.0 years ago by
Sam
▴ 150
8
votes
30
replies
5.0k
views
Per Base Sequence Content
sequencing
fastqc
genome
sequence
updated 4.0 years ago by
wm
▴ 550 • written 4.0 years ago by
Researcher
▴ 20
4
votes
30
replies
2.3k
views
Script makes different file then the manual command, but the command is the same
pipeline
linux
awk
3.7 years ago by
stan.aanhane
▴ 30
14
votes
30
replies
3.3k
views
Download GTF/GFF annotation data for NT database, not by organism (for STAR alignment)
RNA-Seq
rna-seq
alignment
next-gen
4.9 years ago by
Malka
▴ 80
4
votes
30
replies
2.3k
views
SNPs and DEL/MNP in the same position. (DEL or SNP ??)
snp
indels
vcf
calls
mpileup
updated 3.7 years ago by
Ram
43k • written 3.7 years ago by
sami
▴ 30
0
votes
29
replies
2.8k
views
concordance rate between SNP observed and SNP not observed
SNP
updated 5.8 years ago by
Biostar
20 • written 5.9 years ago by
nour.hadjz
▴ 20
11
votes
29
replies
9.6k
views
SummarizedExperiment nrow differs from ncol
DESeq2
SummarizedExperiment
updated 2.4 years ago by
Ram
43k • written 9.8 years ago by
Parham
★ 1.6k
7
votes
29
replies
2.4k
views
What's the powerful biological methods for significant genes selection?
gene selection
significant
biological method
R
5.3 years ago by
Chaimaa
▴ 260
12
votes
28
replies
2.6k
views
Calculating the expression level of genes
Gene expression
RNA-Seq
R
5.8 years ago by
Za
▴ 140
2
votes
28
replies
7.3k
views
Memory use in indexing
Assembly
software error
updated 5.6 years ago by
Ram
43k • written 5.8 years ago by
marongiu.luigi
▴ 710
3
votes
27
replies
5.5k
views
7 follow
Did anyone manage to successfully run HLAScan and get results?
HLA-Typing
NGS
updated 5.6 years ago by
Shiqi Li
• 0 • written 5.8 years ago by
zeynep
▴ 10
9
votes
27
replies
7.4k
views
How do I use Glimmer 3.02?
sequencing
updated 5.2 years ago by
ojelizodun
• 0 • written 6.0 years ago by
nattzy94
▴ 50
4
votes
27
replies
4.2k
views
MISO test run fails error of bam file was not found
RNA-Seq
Assembly
software error
next-gen
genome
updated 3.3 years ago by
Biostar
20 • written 7.6 years ago by
JoeDoasi
▴ 10
1
vote
26
replies
6.0k
views
plink --assoc command gives "NA" for all the analysis (F_A,F_U,A2,CHISQ,P,OR values)
SNP
plink
association
analysis
5.1 years ago by
kushagraprasad24
• 0
3
votes
26
replies
1.8k
views
6 follow
STAR Genome index Error
STAR
updated 5 months ago by
Ram
43k • written 5 months ago by
Prasanna
• 0
8
votes
25
replies
2.9k
views
construction of a database
sql
noSQL
neo4j
database
updated 12 months ago by
Ram
43k • written 2.9 years ago by
Debut
▴ 20
10
votes
25
replies
3.4k
views
The interpretation of PCA
DESeq2
R
PCA
updated 5.7 years ago by
Biostar
20 • written 5.7 years ago by
Za
▴ 140
24
votes
25
replies
7.9k
views
How to generate Beta diversity boxplot from phyloseq object?
phyloseq
beta diversity
metagenomics
3.7 years ago by
dpc
▴ 240
5
votes
24
replies
8.6k
views
Plink1.9 gives error when converting VCF.gz to PED? "Error read failure"
VCF
Plink
5.8 years ago by
DanielC
▴ 160
0
votes
24
replies
3.4k
views
converting spaces to tabs in gtf files
NCBI
2.9 years ago by
storm1907
▴ 30
11
votes
24
replies
5.3k
views
BWA mem skip orientation
assembly
genome
alignment
next-gen
4.9 years ago by
williamsbrian5064
▴ 510
13
votes
24
replies
4.4k
views
Error of bam-to-sam conversion using samtools
samtools
TopHat2
RNA-Seq
BAM
SAM
updated 7.1 years ago by
GenoMax
140k • written 7.1 years ago by
Gary
▴ 480
10
votes
23
replies
2.4k
views
Two simillarly annotated sequence has no alignment similarity. Why?
blast
alignment
gene
updated 6.4 years ago by
GenoMax
140k • written 6.4 years ago by
Farbod
★ 3.4k
1
vote
23
replies
2.0k
views
FASTQ exctract ID's
fastq
4.3 years ago by
User000
▴ 690
1
vote
23
replies
1.7k
views
Parse multifasta files based on a values in two columns in a metadata file
parse
mutlifasta
RefSeq
database
strain
3.6 years ago by
jmwhitha
• 0
6
votes
23
replies
2.9k
views
Could you help me set up a VCF filter?
genome
software error
VCF filter
5.8 years ago by
Charlie2
▴ 50
11
votes
22
replies
4.0k
views
No significant DEG: A request to double check my commands for limma.
limma
differential gene expression
covariates
4.9 years ago by
RNAseqer
▴ 260
23
votes
22
replies
48k
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 16 months ago by
Nicole
• 0 • written 5.9 years ago by
gaelgarcia
▴ 260
4
votes
22
replies
5.3k
views
samtools coverage usage
NGS
updated 2.8 years ago by
Lila M
★ 1.2k • written 2.8 years ago by
smrutimayipanda
▴ 20
1
vote
22
replies
3.4k
views
Genome Index and Alignment- STAR
RNA-Seq
genome
alignment
STAR
updated 5.3 years ago by
Kevin Blighe
87k • written 5.3 years ago by
carolgalah
• 0
3
votes
22
replies
3.0k
views
Making RefSeq in Windows
refseq
7.7 years ago by
Alireza Ebadi Tabrizi
• 0
2
votes
22
replies
2.2k
views
6 follow
Find ~1 Mb regions of genome that are shared by two or more WGS samples?
pedigree
linkage
genetics
17 months ago by
Joel Wallenius
▴ 210
0
votes
22
replies
3.3k
views
Using java Treeview to analyse genes: how to select and compile group of genes to present?
RNA-Seq
6.0 years ago by
Muha0216
• 0
13
votes
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva
combat
batch effects
updated 6.5 years ago by
Biostar
20 • written 6.7 years ago by
lessismore
★ 1.3k
1
vote
22
replies
6.1k
views
how to use faSplit to split fasta into x files
next-gen
faSplit
sequence
5.4 years ago by
olechnwin
▴ 60
5
votes
22
replies
7.4k
views
SVM for classified gene expression data
R
svm
microarray
updated 20 months ago by
Ram
43k • written 8.2 years ago by
Shaurya Jauhari
▴ 50
5
votes
22
replies
3.3k
views
Differential analysis between two cell lines
R
RNA-Seq
edgeR
differential analysis
5.7 years ago by
Biologist
▴ 290
2
votes
21
replies
4.0k
views
Compute the correlations between submatrices
correlation
R
matrix
foreach
updated 5.0 years ago by
Ram
43k • written 5.0 years ago by
pablo
▴ 300
1
vote
21
replies
2.8k
views
Center and scale RIN values for DESeq2?
deseq2
rin
3.6 years ago by
randalljellis
▴ 90
6
votes
21
replies
2.7k
views
How to evaluate the similarity of genes between two sample
RNA-Seq
differential
updated 5.5 years ago by
Biostar
20 • written 5.7 years ago by
afli
▴ 190
16
votes
21
replies
2.1k
views
Why there are different hit for a same gene in different species
gene
blast
ortholog
paralog
7.5 years ago by
Farbod
★ 3.4k
7
votes
21
replies
3.1k
views
Merged.gtf vs. Rnor_6.0.gtf for Raw Counts
RNA-Seq
cuffmerge
raw counts
7.4 years ago by
jmsyl.hong
• 0
3
votes
21
replies
3.7k
views
Normalization agilent microarray data?
Microarray
Normalization
updated 2.9 years ago by
Ram
43k • written 4.5 years ago by
mathavanbioinfo
▴ 80
0
votes
21
replies
2.6k
views
HTSeq-Count: no_feature too high?
htseq-count
17 months ago by
sea.joson
▴ 10
1,000 results • Page
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Recent Votes
C: Why is 0/0 homozygous reference call in VCF useful information?
Answer: snippy error
Answer: TSS of protein coding genes
TSS of protein coding genes
Answer: vcf not indexing
Comment: Hybrid assembly Pacbio- Nanopore
Answer: vg call is time consuming
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Comment: Variant calling of GBS data
by
analyst
▴ 10
It is still giving same warning java -jar -Xmx30G gatk.jar VariantFiltration -R reference.fa -V A_raw_snps.vcf -O A_filtered_snps.vcf --fi…
Comment: Nextflow ERROR : Timeout waiting for connection from pool
by
dzisis1986
▴ 70
It doesn't make sense how to change the threads and in my case it is not working! What kind of problem is that ? is it related to Amazon to…
Comment: STAR aligner options
by
theophile
• 0
I have finally found out the reason behind this behavior. As [pointed out by dsull][1], the beginning of the alignment of read1 to the rat…
Comment: Variant calling of GBS data
by
analyst
▴ 10
Right Pierre, thanks.
Comment: Variant calling of GBS data
by
Pierre Lindenbaum
160k
remove spaces in expressions. 'MQRankSum<0.4'
Comment: Variant calling of GBS data
by
analyst
▴ 10
![enter image description here][1] [1]: /media/images/710829f2-e4af-4743-a31d-822520b4
Comment: Variant calling of GBS data
by
analyst
▴ 10
Vcf file contains this information ![enter image description here][1] [1]: /media/images/b3f699e5-2dd9-4e08-8f5b-2a716544
Comment: Variant calling of GBS data
by
analyst
▴ 10
Command used : **java -jar -Xmx30G gatk.jar VariantFiltration -R reference.fa -V A_raw_snps.vcf -O A_filtered_snps.vcf --filter-name "QD_f…
Comment: Variant calling of GBS data
by
analyst
▴ 10
I am using gatK version 4.2.1.0 for variant filtration but it generates following warnings: 14:10:40.970 WARN JexlEngine - ![0,14]: 'Read…
Comment: STAR aligner options
by
dsull
★ 5.6k
In that first link, Dr. Dobin states how such configurations will "split" the reads into pieces -- exactly what I alluded to in my comment.…
Comment: Nanopore data filtering using fastp
by
emilydolivo97
• 0
thank you for this advice , but when reading the documentation of split2 I found that it generates multiple files for the same fastq file. …
Comment: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
by
ATpoint
81k
I will delete this as it - obviously - does not belong into this thread.
Comment: STAR aligner options
by
theophile
• 0
I searched the different options to increase the sensitivity. As per `--seedSearchStartLmax`, I found several answer from Alexander Dobin o…
Comment: STAR aligner options
by
theophile
• 0
Sorry, I was a bit confused by the layout, thanks for editing and clarifying!
Answer: calculate mismatch rate from VCF file
by
Pierre Lindenbaum
160k
> I want to calculate the mismatch rate on base-level, samtools stats in.bam | grep "error rate" | cut -f 2,3 error rate: 2.0…
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