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41
votes
55
replies
9.1k
views
6 follow
hash function for DNA sequences
hash hashing DNA
6.5 years ago by midox ▴ 290
4
votes
45
replies
5.7k
views
SAM file wrong? help with validatesamfile
EXOME Tutorial
updated 6.1 years ago by 20 • written 6.3 years ago by ▴ 100
19
votes
43
replies
3.6k
views
Annotation of huge number of CNV files
CNV annotation TCGA
4.1 years ago by nazaninhoseinkhan ▴ 460
16
votes
38
replies
15k
views
Differential gene Analysis by Limma
Limma Microarray R
updated 5 months ago by 37k • written 7.6 years ago by ▴ 920
17
votes
37
replies
2.9k
views
No alias or index file found for protein database
next-gen software error sequence
updated 3.4 years ago by 20 • written 3.5 years ago by ▴ 460
3
votes
32
replies
1.9k
views
fastqc report for degradome reads
fastqc adaptor
4.5 years ago by Sam ▴ 150
8
votes
30
replies
3.0k
views
Per Base Sequence Content
sequencing fastqc genome sequence
updated 2.5 years ago by ▴ 540 • written 2.5 years ago by ▴ 20
4
votes
30
replies
1.0k
views
Script makes different file then the manual command, but the command is the same
pipeline linux awk
2.3 years ago by stan.aanhane ▴ 30
14
votes
30
replies
2.2k
views
Download GTF/GFF annotation data for NT database, not by organism (for STAR alignment)
RNA-Seq rna-seq alignment next-gen
3.4 years ago by Malka ▴ 70
4
votes
30
replies
1.1k
views
SNPs and DEL/MNP in the same position. (DEL or SNP ??)
snp indels vcf calls mpileup
updated 2.2 years ago by 37k • written 2.2 years ago by ▴ 30
11
votes
29
replies
7.4k
views
SummarizedExperiment nrow differs from ncol
DESeq2 SummarizedExperiment
updated 11 months ago by 37k • written 8.3 years ago by ★ 1.6k
0
votes
29
replies
1.8k
views
concordance rate between SNP observed and SNP not observed
SNP
updated 4.3 years ago by 20 • written 4.4 years ago by ▴ 20
7
votes
29
replies
1.3k
views
What's the powerful biological methods for significant genes selection?
gene selection significant biological method R
3.9 years ago by Chaimaa ▴ 260
12
votes
28
replies
1.6k
views
Calculating the expression level of genes
Gene expression RNA-Seq R
4.3 years ago by Za ▴ 140
2
votes
28
replies
4.6k
views
Memory use in indexing
Assembly software error
updated 4.2 years ago by 37k • written 4.3 years ago by ▴ 660
9
votes
27
replies
5.4k
views
How do I use Glimmer 3.02?
sequencing
updated 3.7 years ago by • 0 • written 4.6 years ago by ▴ 50
3
votes
27
replies
4.2k
views
7 follow
Did anyone manage to successfully run HLAScan and get results?
HLA-Typing NGS
updated 4.2 years ago by • 0 • written 4.3 years ago by ▴ 10
4
votes
27
replies
3.2k
views
MISO test run fails error of bam file was not found
RNA-Seq Assembly software error next-gen genome
updated 22 months ago by 20 • written 6.1 years ago by ▴ 10
1
vote
26
replies
3.8k
views
plink --assoc command gives "NA" for all the analysis (F_A,F_U,A2,CHISQ,P,OR values)
SNP plink association analysis
3.6 years ago by kushagraprasad24 • 0
10
votes
25
replies
2.4k
views
The interpretation of PCA
DESeq2 R PCA
updated 4.2 years ago by 20 • written 4.3 years ago by ▴ 140
8
votes
25
replies
1.6k
views
construction of a database
neo4j noSQL sql bioinformatic database
updated 16 months ago by 52k • written 16 months ago by ▴ 40
24
votes
25
replies
4.8k
views
How to generate Beta diversity boxplot from phyloseq object?
phyloseq beta diversity metagenomics
2.2 years ago by dpc ▴ 240
11
votes
24
replies
3.5k
views
BWA mem skip orientation
assembly genome alignment next-gen
3.4 years ago by williamsbrian5064 ▴ 460
5
votes
24
replies
6.2k
views
Plink1.9 gives error when converting VCF.gz to PED? "Error read failure"
VCF Plink
4.3 years ago by DanielC ▴ 150
13
votes
24
replies
2.9k
views
Error of bam-to-sam conversion using samtools
samtools TopHat2 RNA-Seq BAM SAM
updated 5.6 years ago by 121k • written 5.6 years ago by ▴ 480
0
votes
24
replies
2.2k
views
converting spaces to tabs in gtf files
NCBI
17 months ago by storm1907 ▴ 30
6
votes
23
replies
1.9k
views
Could you help me set up a VCF filter?
genome software error VCF filter
4.3 years ago by Charlie2 ▴ 50
1
vote
23
replies
828
views
FASTQ exctract ID's
fastq
2.8 years ago by User000 ▴ 580
10
votes
23
replies
1.6k
views
Two simillarly annotated sequence has no alignment similarity. Why?
blast alignment gene
updated 4.9 years ago by 121k • written 4.9 years ago by ★ 3.3k
1
vote
23
replies
814
views
Parse multifasta files based on a values in two columns in a metadata file
parse mutlifasta RefSeq database strain
2.1 years ago by jmwhitha • 0
11
votes
22
replies
2.5k
views
No significant DEG: A request to double check my commands for limma.
limma differential gene expression covariates
3.4 years ago by RNAseqer ▴ 200
5
votes
22
replies
2.2k
views
Differential analysis between two cell lines
R RNA-Seq edgeR differential analysis
4.2 years ago by Biologist ▴ 260
5
votes
22
replies
6.0k
views
SVM for classified gene expression data
R svm microarray
updated 9 weeks ago by 37k • written 6.7 years ago by ▴ 50
0
votes
22
replies
2.3k
views
Using java Treeview to analyse genes: how to select and compile group of genes to present?
RNA-Seq
4.5 years ago by Muha0216 • 0
3
votes
22
replies
1.7k
views
samtools coverage usage
NGS
updated 15 months ago by ★ 1.2k • written 15 months ago by ▴ 20
3
votes
22
replies
2.2k
views
Making RefSeq in Windows
refseq
6.2 years ago by Alireza Ebadi Tabrizi • 0
13
votes
22
replies
8.3k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva combat batch effects
updated 5.0 years ago by 20 • written 5.2 years ago by ★ 1.3k
1
vote
22
replies
4.2k
views
how to use faSplit to split fasta into x files
next-gen faSplit sequence
3.9 years ago by olechnwin ▴ 60
1
vote
22
replies
2.0k
views
Genome Index and Alignment- STAR
RNA-Seq genome alignment STAR
updated 3.9 years ago by 83k • written 3.9 years ago by • 0
2
votes
21
replies
2.4k
views
Compute the correlations between submatrices
correlation R matrix foreach
updated 3.5 years ago by 37k • written 3.5 years ago by ▴ 230
23
votes
21
replies
33k
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
4.4 years ago by gaelgarcia ▴ 250
16
votes
21
replies
1.4k
views
Why there are different hit for a same gene in different species
gene blast ortholog paralog
6.0 years ago by Farbod ★ 3.3k
7
votes
21
replies
2.1k
views
Merged.gtf vs. Rnor_6.0.gtf for Raw Counts
RNA-Seq cuffmerge raw counts
5.9 years ago by jmsyl.hong • 0
6
votes
21
replies
1.8k
views
How to evaluate the similarity of genes between two sample
RNA-Seq differential
updated 4.0 years ago by 20 • written 4.2 years ago by ▴ 190
10
votes
21
replies
2.0k
views
Calculate disease risk based on the genoytype of some SNPs?
SNP prs gwas PRSice Plink
updated 3.2 years ago by 20 • written 3.2 years ago by ▴ 10
1
vote
21
replies
1.5k
views
Center and scale RIN values for DESeq2?
deseq2 rin
2.1 years ago by randalljellis ▴ 90
3
votes
21
replies
2.4k
views
Normalization agilent microarray data?
Microarray Normalization
updated 17 months ago by 37k • written 3.0 years ago by ▴ 60
4
votes
20
replies
985
views
How can I count aminoacid residues from a HUGE compressed fasta file?
sequence
2.7 years ago by schlogl ▴ 120
5
votes
20
replies
6.9k
views
How to plot ChIP-seq Density vs Distance from TSS using Homer annoted files
ChIP-Seq homer
6.2 years ago by varsha619 ▴ 90
8
votes
20
replies
1.6k
views
Converting runpsipred Script to Work on Windows OS
psipred windows
updated 4 months ago by 37k • written 4.2 years ago by ▴ 270
1,000 results • Page 1 of 20
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Answer: RefSeq Transcript vs Reference Genome sequence
Answer: Conceptual phylogenetics questions
StringTie --merge creates the same id for neighbouring genes
Answer: Conceptual phylogenetics questions
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Answer: Conceptual phylogenetics questions
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Recent Replies
Comment: preforming armitage test on chunks of data in R of VCF file by Eliza • 0
@rpolicastro during wrapup: 0 (non-NA) cases Error: no more error handlers available (recursive errors?); invoking 'abort' restart
Comment: Tools for generating realistic rna-seq reads from reference transcriptome by GenoMax 121k
Any read simulation tool should work. `ART `(https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm ) `randomrea…
Answer: RefSeq Transcript vs Reference Genome sequence by Jeremy ▴ 600
The transcript is the RNA sequence, while the genome sequence is the genomic DNA sequence.
Answer: RefSeq Transcript vs Reference Genome sequence by GenoMax 121k
RefSeq transcripts are expressed part of the genome. Refseq genome is the entire genome sequence.
Answer: SRA-tools retrieved data of different size compared to ncbi website by GenoMax 121k
Never use file sizes as a metric for anything other than for qualitative purpose (e.g. a file is non-zero bytes so must have something). …
Comment: Calculating fragment start and end in python by mhasa006 ▴ 70
Well, that is true, but it is part of a bigger project. And calling third-party tools can be problematic. Either way, thanks for the reply.
Comment: Calculating fragment start and end in python by mhasa006 ▴ 70
Thanks for the reply, will try that.
Comment: Calculating fragment start and end in python by iraun 4.8k
Do you need to to this in python? There are tools already out there performing these kind of tasks, such as [CollectInsertSizeMetrics (pica…
Comment: Calculating fragment start and end in python by jv ▴ 550
how about filtering the BAM file for the region on interest and then converting the output to a BED file which will contain the read start …
Comment: Calculating fragment start and end in python by mhasa006 ▴ 70
Actually, I'm fetching reads form a BAM file that is within a bed region. Then I'm trying to calculate the fragment start/end of the fetche…
Comment: Calculating fragment start and end in python by jv ▴ 550
would `bedtools bamtobed` get you what you want? <https://bedtools.readthedocs.io/en/latest/content/tools/bamtobed.html>
Comment: preforming armitage test on chunks of data in R of VCF file by rpolicastro 10.0k
This can also be done with list columns but I think splitting the data is a little syntactically clearer. ``` library("dplyr") library("CAT…
Comment: preforming armitage test on chunks of data in R of VCF file by Eliza • 0
@rpolicastro on data frame format
Comment: genotype encoding by Eliza • 0
@David Carlson . doea it mean that if i have a file that contains ony SNPs the encoding cant be zero?"A site with a homozygous reference ge…
Comment: preforming armitage test on chunks of data in R of VCF file by rpolicastro 10.0k
Are you doing this on a VCF or the data format in the screenshot?
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