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1,000 results • Page 2 of 20
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12
votes
10
replies
4.1k
views
Speed up BLASTp vs NCBI nr database
blast
7.9 years ago by biotech ▴ 570
12
votes
28
replies
2.7k
views
Calculating the expression level of genes
Gene expression RNA-Seq R
5.9 years ago by Za ▴ 140
12
votes
8
replies
1.3k
views
Align 16S sequence to a reference
16S sequence alignment
updated 19 months ago by 4.5k • written 19 months ago by ▴ 160
12
votes
8
replies
3.1k
views
How to change depth of sequence in RNA-seq fastq files
depth of sequence RNA-Seq
7.2 years ago by statfa ▴ 760
12
votes
17
replies
4.8k
views
How do I generate all possible Newick Tree permutations for a set of species given an outgroup in Python?
Python Newick phylogenetics tree phylogeny
6.5 years ago by anonymous1192976466 ▴ 50
12
votes
14
replies
5.7k
views
bedtools intersect error?
ChIP-Seq bedtools intersect
5.2 years ago by star ▴ 350
12
votes
21
replies
3.2k
views
Calculate disease risk based on the genoytype of some SNPs?
SNP prs gwas PRSice Plink
updated 4.7 years ago by 20 • written 4.7 years ago by ▴ 30
12
votes
10
replies
2.9k
views
7 follow
SAM / BAM alignments
SAM BAM
7.3 years ago by John 13k
12
votes
13
replies
2.7k
views
Gene Expression and Systems Biology (homework)
gene homework
updated 16 months ago by 43k • written 8.8 years ago by • 0
11
votes
22
replies
4.1k
views
No significant DEG: A request to double check my commands for limma.
limma differential-gene-expression
updated 8 days ago by 43k • written 5.0 years ago by ▴ 260
11
votes
10
replies
10k
views
Extracting from tophat outputs reads pairs and splice-junctions with a single best match
TOPHAT RNA-Seq
updated 2.3 years ago by 43k • written 9.7 years ago by ▴ 160
11
votes
12
replies
1.4k
views
Need help changing RNA-seq code from histat aligner into Star aligner please.
RNA-Seq
3.8 years ago by screadore ▴ 20
11
votes
2
replies
1.5k
views
Concept behind p-value correction?
RNA-Seq protemics genome R
4.7 years ago by WUSCHEL ▴ 750
11
votes
3
replies
942
views
How to deal with the probe id mapping to multiple gene ids?
match microarray affymetrix probe gene
12 months ago by DareDevil ★ 4.3k
11
votes
11
replies
1.0k
views
6 follow
Doubt regarding dna sequence length
genome sequencing sequence
4.0 years ago by lokeshp14cs24 • 0
11
votes
9
replies
2.5k
views
samtools piping with awk/ bash commands -> Wonky things happen!!!
bash samtools awk
updated 16 months ago by 43k • written 8.8 years ago by ★ 2.5k
11
votes
10
replies
1.6k
views
Most fishes lay eggs, some are live-bearing, How to find related genes to these different charachteristics?
gene reproduction evolution alignment
updated 7.6 years ago by 20 • written 7.6 years ago by ★ 3.4k
11
votes
7
replies
3.3k
views
Estimating Mean Inner Distance
tuxedo tophat RNA-Seq
7.4 years ago by CF ▴ 50
11
votes
11
replies
5.6k
views
6 follow
How to get work experience in Bioinformatics
work experience python genome sequence
6.1 years ago by ishackm ▴ 110
11
votes
6
replies
3.2k
views
Understanding Supplementary reads.
Bowtie2 MEM BWA Dragen
updated 2.2 years ago by 100k • written 2.2 years ago by ▴ 10
11
votes
5
replies
1.3k
views
Differential expression analysis - issue with replicating results
rnaseq DESeq2 R bioconductor
updated 2.4 years ago by 81k • written 2.4 years ago by ▴ 10
11
votes
11
replies
2.7k
views
Error of Groups in R
affy limma oligo bioconductor R
updated 7.9 years ago by 20 • written 7.9 years ago by ▴ 70
11
votes
24
replies
5.4k
views
BWA mem skip orientation
assembly genome alignment next-gen
5.0 years ago by williamsbrian5064 ▴ 510
11
votes
10
replies
5.7k
views
Best mapping software to generate BAM file
BAM mapping
updated 6.4 years ago by 20 • written 6.5 years ago by ▴ 630
11
votes
10
replies
2.8k
views
6 follow
Genomic statistics from gtf
gene gtf
5.8 years ago by plebaninora • 0
11
votes
6
replies
6.3k
views
Merging raw Illumina FASTQ files with snakemake
snakemake illumina paired-end reads
6.8 years ago by Jokhe ▴ 140
11
votes
4
replies
2.6k
views
10 to 1000X speedup of BWA read alignment trough compressive mapping: MIT CORA
bwa fastq alignment compression
updated 7.8 years ago by 20 • written 8.0 years ago by ★ 5.3k
11
votes
29
replies
9.7k
views
SummarizedExperiment nrow differs from ncol
DESeq2 SummarizedExperiment
updated 2.5 years ago by 43k • written 9.9 years ago by ★ 1.6k
11
votes
15
replies
2.8k
views
How do I get the read counts for a specific exon
bam exon
updated 6.1 years ago by 43k • written 6.1 years ago by ▴ 30
10
votes
8
replies
6.1k
views
Software To Calculate Power Of Exome Sequencing?
exome statistics
updated 12.6 years ago by 49k • written 12.6 years ago by ▴ 300
10
votes
1
reply
4.0k
views
Assessing The Quality Of Mirna Rnaseq Data
mirna
updated 10.4 years ago by 20 • written 11.1 years ago by 12k
10
votes
3
replies
1.4k
views
how to create new file
r
updated 7.4 years ago by 141k • written 7.4 years ago by ▴ 80
10
votes
6
replies
8.3k
views
Any idea how to solve this error in fgsea - "Error in if (any(simpleFgseaRes$modeFraction < 10)) { : missing value where TRUE/FALSE needed"?
fgsea
updated 2.8 years ago by ▴ 920 • written 2.8 years ago by ▴ 10
10
votes
11
replies
4.7k
views
Trouble Installing Genometools-1.5.1 On My Mac Ox
genome protein-structure
10.2 years ago by inadamj ▴ 60
10
votes
14
replies
4.9k
views
ATAC-seq data and deepTools: Small detail with impact on output
bigwig read-length deeptools ATAC-seq
updated 10 months ago by 43k • written 4.2 years ago by ▴ 50
10
votes
5
replies
2.4k
views
error with samtools
RNA-Seq
updated 7.2 years ago by 20 • written 7.3 years ago by ▴ 20
10
votes
15
replies
1.7k
views
Can't find a variant which suppose must have in a vcf file
variant-calling bcftools nf-core
9 months ago by Chris ▴ 260
10
votes
8
replies
1.7k
views
File Format - Fasta
sequence
8.1 years ago by Gabe Anderson ▴ 10
10
votes
10
replies
3.8k
views
Parameter optimization STAR
RNA-Seq
6.2 years ago by XBria ▴ 90
10
votes
2
replies
595
views
any script that can do this task
shell-script
updated 2.1 years ago by 43k • written 2.1 years ago by ▴ 20
10
votes
7
replies
1.2k
views
Can two mates have different file size?
sequencing fastq
5.7 years ago by marongiu.luigi ▴ 710
10
votes
6
replies
962
views
RNA seq, secreted protein
protein gene secreted
updated 8 months ago by 21k • written 16 months ago by ▴ 170
10
votes
15
replies
6.2k
views
convert fasta/gb to vcf
fasta vcf genbank gff
updated 13 months ago by 43k • written 5.5 years ago by ▴ 710
10
votes
19
replies
3.4k
views
What is a difference between uniprot and 'nr. Non-redundant GenBank...'?
Genebank blast UniProt
updated 2.9 years ago by 141k • written 2.9 years ago by ▴ 20
10
votes
11
replies
9.1k
views
How to adjust my manhattan plot to look better?
qqman manhattan R
updated 22 months ago by 43k • written 9.1 years ago by ▴ 40
10
votes
9
replies
2.0k
views
How to improve fastq quality based on fastqc output ?
RNA-Seq
5.9 years ago by Angelique ▴ 10
10
votes
11
replies
1.6k
views
How to identify dysregulated pathways using Support Vector machine (SVM)?
SVM
5.3 years ago by Chaimaa ▴ 260
10
votes
7
replies
1.2k
views
Better DE analytic tools
RNA-Seq DE tools Bayesian empirical approach
5.9 years ago by mhyunjunkang ▴ 110
10
votes
2
replies
2.8k
views
Standalone Blast Issue
blast
11.9 years ago by chlazaris • 0
10
votes
4
replies
1.4k
views
How to pipe samtools mileup with varscan trio caller?
varscan samtools pipe
3.3 years ago by DareDevil ★ 4.3k
1,000 results • Page 2 of 20
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Error with Formatdb of legacy blast?
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A: Ribo-seq vs RNA-seq read count
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Recent Replies
Comment: ISCN annotation for SV/CN VCF files by adedare • 0
https://res.saletool.cn/vcf/18084521725806
Comment: ISCN annotation for SV/CN VCF files by adedare • 0
https://res.saletool.cn/vcf/18084435127462
Comment: How can I solve this error? by 22211020193 • 0
I want to conduct GWAS meta-analysis using metal software.
Comment: How to reduce the variation of CIBERSORTx results? by feather-W • 0
Hi LChart, Thanks for your reply. Yes, the identical command lines produce different results in CIBERSORTx S-mode. Although I input the da…
Comment: Removing duplicates by joe ▴ 490
I *could* imagine an ONT scenario where you'd want to remove duplicates (amplicon-seq, etc) but likely for variant calling there is no need…
Comment: Removing duplicates by samuel.a.odonnell ▴ 510
As above, you do not need to worry about duplicates for ONT data Also have you looked at using other tools for variant calling more suited…
Answer: Pediococcus acidilactici sequence analysis by geneontologyhelp ▴ 340
If you're looking for the GO annotations for *Pediococcus acidilactici*, these are available. Using the instructions under [*2. All other…
Answer: What is the normalization status of metabric data? by etiennedanis ▴ 10
I just found an answer to this question here: [https://groups.google.com/g/cbioportal/c/hm_i4jbG1uc/m/h9rNYOvpAAAJ][1] [1]: https://gro…
Comment: Removing duplicates by joe ▴ 490
With ONT you will only have PCR duplicates. 'Read' (you mean optical?) duplicates are an artifact of cluster-based sequencing (ie Illumina)…
Comment: assembly using CCS, CLR, CCS_CLR sequences together? by GenoMax 141k
PacBio has some recommendations on software for genome assemblies on this page (which you may have seen but just in case): https://www.pacb…
Answer: DEG analysis of RNA-seq data across multiple tissues and two conditions by swbarnes2 14k
I would not put totally different tissues in the same DESeq object. I don't think that's going to do good things for normalization or disp…
Comment: Removing duplicates by quentinperriere • 0
pcr duplicates or/and read duplicates should I use this command to remove them ? or we don't talk about duplicates when dealing with ONT ??…
Comment: How to reduce the variation of CIBERSORTx results? by LChart 3.9k
If you didn't change the input signature matrix, the input RNA matrix, or the input parameters - what did you change? Is the statement that…
Answer: Inconsistency in SNP detection pipelines for multi-sample analysis by LChart 3.9k
> To replicate GVCF behavior and avoid issues with 0/0 genotypes appearing as missing, I don't use the -v option I'm not sure what you m…
Comment: Supergnova stuck in tutorial by GenoMax 141k
Your best option may be to email the author (and/or the senior author from the paper). Let them know that the FTP links mentioned on GitHub…
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