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41
votes
55
replies
10k
views
6 follow
hash function for DNA sequences
hash hashing DNA
7.2 years ago by midox ▴ 290
4
votes
45
replies
6.3k
views
SAM file wrong? help with validatesamfile
EXOME
updated 8 weeks ago by 39k • written 6.9 years ago by ▴ 110
19
votes
43
replies
4.2k
views
Annotation of huge number of CNV files
CNV annotation TCGA
4.8 years ago by nazaninhoseinkhan ▴ 510
16
votes
38
replies
16k
views
Differential gene Analysis by Limma
Limma Microarray R
updated 13 months ago by 39k • written 8.3 years ago by ▴ 920
17
votes
37
replies
3.5k
views
No alias or index file found for protein database
next-gen software error sequence
updated 4.0 years ago by 20 • written 4.2 years ago by ▴ 470
3
votes
32
replies
2.6k
views
fastqc report for degradome reads
fastqc adaptor
5.2 years ago by Sam ▴ 150
8
votes
30
replies
3.9k
views
Per Base Sequence Content
sequencing fastqc genome sequence
updated 3.2 years ago by ▴ 550 • written 3.2 years ago by ▴ 20
14
votes
30
replies
2.6k
views
Download GTF/GFF annotation data for NT database, not by organism (for STAR alignment)
RNA-Seq rna-seq alignment next-gen
4.1 years ago by Malka ▴ 70
4
votes
30
replies
1.4k
views
Script makes different file then the manual command, but the command is the same
pipeline linux awk
2.9 years ago by stan.aanhane ▴ 30
4
votes
30
replies
1.6k
views
SNPs and DEL/MNP in the same position. (DEL or SNP ??)
snp indels vcf calls mpileup
updated 2.8 years ago by 39k • written 2.8 years ago by ▴ 30
11
votes
29
replies
8.3k
views
SummarizedExperiment nrow differs from ncol
DESeq2 SummarizedExperiment
updated 19 months ago by 39k • written 9.0 years ago by ★ 1.6k
7
votes
29
replies
1.7k
views
What's the powerful biological methods for significant genes selection?
gene selection significant biological method R
4.5 years ago by Chaimaa ▴ 260
0
votes
29
replies
2.2k
views
concordance rate between SNP observed and SNP not observed
SNP
updated 5.0 years ago by 20 • written 5.1 years ago by ▴ 20
2
votes
28
replies
5.6k
views
Memory use in indexing
Assembly software error
updated 4.8 years ago by 39k • written 5.0 years ago by ▴ 680
12
votes
28
replies
1.9k
views
Calculating the expression level of genes
Gene expression RNA-Seq R
5.0 years ago by Za ▴ 140
9
votes
27
replies
6.3k
views
How do I use Glimmer 3.02?
sequencing
updated 4.4 years ago by • 0 • written 5.2 years ago by ▴ 50
4
votes
27
replies
3.7k
views
MISO test run fails error of bam file was not found
RNA-Seq Assembly software error next-gen genome
updated 2.5 years ago by 20 • written 6.8 years ago by ▴ 10
3
votes
27
replies
4.8k
views
7 follow
Did anyone manage to successfully run HLAScan and get results?
HLA-Typing NGS
updated 4.8 years ago by • 0 • written 5.0 years ago by ▴ 10
1
vote
26
replies
4.8k
views
plink --assoc command gives "NA" for all the analysis (F_A,F_U,A2,CHISQ,P,OR values)
SNP plink association analysis
4.3 years ago by kushagraprasad24 • 0
24
votes
25
replies
6.2k
views
How to generate Beta diversity boxplot from phyloseq object?
phyloseq beta diversity metagenomics
2.9 years ago by dpc ▴ 240
8
votes
25
replies
2.1k
views
construction of a database
sql noSQL neo4j database
updated 10 weeks ago by 39k • written 2.0 years ago by ▴ 20
10
votes
25
replies
2.7k
views
The interpretation of PCA
DESeq2 R PCA
updated 4.9 years ago by 20 • written 4.9 years ago by ▴ 140
0
votes
24
replies
2.7k
views
converting spaces to tabs in gtf files
NCBI
2.1 years ago by storm1907 ▴ 30
5
votes
24
replies
7.2k
views
Plink1.9 gives error when converting VCF.gz to PED? "Error read failure"
VCF Plink
5.0 years ago by DanielC ▴ 160
13
votes
24
replies
3.5k
views
Error of bam-to-sam conversion using samtools
samtools TopHat2 RNA-Seq BAM SAM
updated 6.2 years ago by 129k • written 6.2 years ago by ▴ 480
11
votes
24
replies
4.2k
views
BWA mem skip orientation
assembly genome alignment next-gen
4.1 years ago by williamsbrian5064 ▴ 470
1
vote
23
replies
1.1k
views
Parse multifasta files based on a values in two columns in a metadata file
parse mutlifasta RefSeq database strain
2.8 years ago by jmwhitha • 0
10
votes
23
replies
1.8k
views
Two simillarly annotated sequence has no alignment similarity. Why?
blast alignment gene
updated 5.5 years ago by 129k • written 5.5 years ago by ★ 3.4k
1
vote
23
replies
1.2k
views
FASTQ exctract ID's
fastq
3.5 years ago by User000 ▴ 660
6
votes
23
replies
2.2k
views
Could you help me set up a VCF filter?
genome software error VCF filter
4.9 years ago by Charlie2 ▴ 50
11
votes
22
replies
3.0k
views
No significant DEG: A request to double check my commands for limma.
limma differential gene expression covariates
4.1 years ago by RNAseqer ▴ 240
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 6 months ago by • 0 • written 5.1 years ago by ▴ 250
5
votes
22
replies
2.6k
views
Differential analysis between two cell lines
R RNA-Seq edgeR differential analysis
4.9 years ago by Biologist ▴ 280
0
votes
22
replies
2.6k
views
Using java Treeview to analyse genes: how to select and compile group of genes to present?
RNA-Seq
5.2 years ago by Muha0216 • 0
1
vote
22
replies
2.6k
views
Genome Index and Alignment- STAR
RNA-Seq genome alignment STAR
updated 4.5 years ago by 85k • written 4.5 years ago by • 0
3
votes
22
replies
2.5k
views
Making RefSeq in Windows
refseq
6.8 years ago by Alireza Ebadi Tabrizi • 0
2
votes
22
replies
1.3k
views
6 follow
Find ~1 Mb regions of genome that are shared by two or more WGS samples?
pedigree linkage genetics
7 months ago by Joel Wallenius ▴ 130
13
votes
22
replies
9.2k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva combat batch effects
updated 5.7 years ago by 20 • written 5.9 years ago by ★ 1.3k
1
vote
22
replies
5.0k
views
how to use faSplit to split fasta into x files
next-gen faSplit sequence
4.6 years ago by olechnwin ▴ 60
4
votes
22
replies
2.9k
views
samtools coverage usage
NGS
updated 23 months ago by ★ 1.2k • written 23 months ago by ▴ 20
5
votes
22
replies
6.6k
views
SVM for classified gene expression data
R svm microarray
updated 10 months ago by 39k • written 7.4 years ago by ▴ 50
2
votes
21
replies
3.0k
views
Compute the correlations between submatrices
correlation R matrix foreach
updated 4.2 years ago by 39k • written 4.2 years ago by ▴ 250
6
votes
21
replies
2.1k
views
How to evaluate the similarity of genes between two sample
RNA-Seq differential
updated 4.7 years ago by 20 • written 4.8 years ago by ▴ 190
10
votes
21
replies
2.4k
views
Calculate disease risk based on the genoytype of some SNPs?
SNP prs gwas PRSice Plink
updated 3.8 years ago by 20 • written 3.9 years ago by ▴ 10
16
votes
21
replies
1.6k
views
Why there are different hit for a same gene in different species
gene blast ortholog paralog
6.7 years ago by Farbod ★ 3.4k
0
votes
21
replies
1.7k
views
HTSeq-Count: no_feature too high?
htseq-count
7 months ago by sea.joson ▴ 10
3
votes
21
replies
3.0k
views
Normalization agilent microarray data?
Microarray Normalization
updated 2.1 years ago by 39k • written 3.7 years ago by ▴ 70
1
vote
21
replies
2.0k
views
Center and scale RIN values for DESeq2?
deseq2 rin
2.8 years ago by randalljellis ▴ 90
7
votes
21
replies
2.4k
views
Merged.gtf vs. Rnor_6.0.gtf for Raw Counts
RNA-Seq cuffmerge raw counts
6.6 years ago by jmsyl.hong • 0
22
votes
20
replies
2.1k
views
what is the prefered strategy to treat with blast-less transcriptomes from RNA-seq
blast RNA-Seq genome gene
updated 8 weeks ago by 39k • written 6.9 years ago by ★ 3.4k
1,000 results • Page 1 of 20
Recent Votes
Comment: Help with running ATAC using Encode pipeline
Answer: I have one fasta file of a bacteria. Can i use to create a phylogenetic tree?
Comment: RNASeq gene labeling and mRNA filter from bulkRNA data.
[Meta] Use of AI
Answer: Network cross-validation
Answer: Random dataset and DESeq2
A: Single end or paired end for variant calling
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Recent Replies
Answer: Is a human genome file with reference as NCBI37 the same as hg19? by GenoMax 129k
If you go to the GRCh37 page at NCBI you will see that `hg19` is a synonym (mostly used by UCSC as I recall): https://www.ncbi.nlm.nih.gov/…
Comment: Help with running ATAC using Encode pipeline by Chris ▴ 100
So do we have redundant in this case when we specify the path to fastq.gz files in both input file and json file? json file is .json, how a…
Comment: Is a human genome file with reference as NCBI37 the same as hg19? by a5864557 • 0
Note: I've also asked this [here][1] [1]: https://bioinformatics.stackexchange.com/questions/21101/is-a-human-genome-file-with-referenc…
Answer: [Meta] Use of AI by GenoMax 129k
As you indicate, AI in some form or other is here to stay and we can't avoid it in our lives and on biostars. Main issue I see is the vali…
Answer: RNASeq gene labeling and mRNA filter from bulkRNA data. by rfran010 ▴ 110
featureCounts can extract this information and output a column for you during counting, presuming you input a GTF file. `extraAttributes …
Comment: What are recommended parameters for the local protein alignment ? by Alexander ▴ 70
Trying to do so ))
Comment: Help with running ATAC using Encode pipeline by rfran010 ▴ 110
The "Input files" section is details on how you can specify your fastqs in the JSON. (You specify all pipeline parameters in the JSON.) Ess…
Comment: What are recommended parameters for the local protein alignment ? by Vincent Laufer ★ 2.9k
does this mean you understand pident now and are moving forward?
Answer: Random dataset and DESeq2 by Vincent Laufer ★ 2.9k
@e38da452 Not only is this not surprising, it is the basis for an entire class of statistical techniques referred to as permutation bas…
Comment: (ERR): "index/Trinity.fa" does not exist or is not a Bowtie 2 index Exiting now by GenoMax 129k
> This generated multiple Trinity.fa files in the index folder Did the process complete successfully?
Comment: Random dataset and DESeq2 by LChart 2.6k
I don't think you've given enough detail about your approach (what's the data? are you correcting for covariates? how did you shuffle? how …
Answer: Network cross-validation by LChart 2.6k
What do you mean by "robust" in this case? Which of the following is closest to what you want to estimate: (1) Would I get a similar res…
Comment: I have one fasta file of a bacteria. Can i use to create a phylogenetic tree? by Mustafa • 0
Thank you so much ! will try them all !
Answer: I have one fasta file of a bacteria. Can i use to create a phylogenetic tree? by andres.firrincieli 3.3k
If the fasta file contains the genome sequence you can use the following: 1. GToTree (see example [here][1]) 2. [GTDB-tk][2] *de novo…
Comment: Low mapping percentage by Sib ▴ 40
Thank you for the reply @genomax . If there is not much I can do about the contamination at this stage, what is the benefit of knowing the…
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