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1,000 results • Page 3 of 20
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10
votes
15
replies
6.2k
views
DIAMOND blast imported into MEGAN6 has no taxonomic assignment
blast MEGAN6 Taxonomy DIAMOND
7.4 years ago by Farbod ★ 3.4k
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
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
5
replies
5.5k
views
Intron Retention And Alternative 5'3' Splice Site Identification
updated 10.2 years ago by 20 • written 13.0 years ago by 2.4k
10
votes
7
replies
3.7k
views
What is Pathway Analysis?
database analysis ontology pathway
updated 10 months ago by 43k • written 8.0 years ago by ▴ 330
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 141k • written 6.4 years ago by ★ 3.4k
10
votes
12
replies
2.0k
views
The 2013 Eisenberg and Levanon housekeeping genes list for Human is the most updated one?
genes human housekeeping list
5.2 years ago by msimmer92 ▴ 300
10
votes
10
replies
2.0k
views
Minor allele frequency
GWAS SNPs Alleles
updated 5.4 years ago by 20 • written 7.4 years ago by ▴ 420
10
votes
1
reply
3.5k
views
RNA-SeQC, EVER-seq, RSeQC and CollectRnaSeqMetrics, which to use and *why*?
RNA-Seq qc
updated 20 months ago by 43k • written 8.9 years ago by ★ 2.6k
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
13
replies
5.8k
views
How to identify DE lncRNA from RNA Seq Data?
RNA-Seq lncrna
7.2 years ago by Vasu ▴ 770
10
votes
25
replies
3.5k
views
The interpretation of PCA
DESeq2 R PCA
updated 5.8 years ago by 20 • written 5.8 years ago by ▴ 140
9
votes
13
replies
3.4k
views
Python Script to map reads to reference sequence
sequence python mapping script reference sequence
5.0 years ago by Fid_o ▴ 40
9
votes
5
replies
1.2k
views
how to retrieve all proteins related to cancer
proteins
7.9 years ago by Learner ▴ 280
9
votes
7
replies
3.3k
views
Aligning Miseq With Deletions >10 Bases
alignment miseq next-gen
updated 10.8 years ago by 20 • written 11.3 years ago by 4.2k
9
votes
13
replies
1.6k
views
SNP's and Gene?
SNP gene
4.5 years ago by imgapgenomika ▴ 10
9
votes
10
replies
2.8k
views
About GATK4 Mutect2 runtime (Whole Exome seq)
GATK Whole Exome Sequencing Mutect2
3.3 years ago by kwanghoon ▴ 20
9
votes
5
replies
3.9k
views
What's the interpretation behind Pathway enrichment analysis
networks pathway enrichment analysis gene
updated 6.6 years ago by 20 • written 6.8 years ago by ▴ 260
9
votes
16
replies
1.9k
views
feature extraction from SNPs in R
R gene sequence SNP
5.5 years ago by bioinfo456 ▴ 150
9
votes
19
replies
2.3k
views
There are any way to use a script for feed emboss with fasta sequence?
sequence
4.3 years ago by schlogl ▴ 160
9
votes
13
replies
2.8k
views
qRT-PCR data analysis steps and workflow
qRT-PCR Reference genes Normalization DeltaCt FC
5.2 years ago by mohammedtoufiq91 ▴ 250
9
votes
20
replies
4.2k
views
Solve SAM issues flagged by Picard's ValidateSamFile
Picard SAM
updated 13 months ago by 43k • written 5.7 years ago by ▴ 710
9
votes
11
replies
8.2k
views
8 follow
Extremely low mapping rates with bowtie2
alignment next-gen
updated 6.5 years ago by 20 • written 6.6 years ago by ▴ 10
9
votes
13
replies
2.4k
views
Reannotating a gene: Identifying translation and transcription start sites
RNA-Seq genome gene
7.3 years ago by rh5118 ▴ 40
9
votes
10
replies
1.9k
views
How to use Poisson distribution to get meaningful expression counts?
statistics rna-seq
updated 2.8 years ago by 19k • written 2.8 years ago by ▴ 520
9
votes
8
replies
1.7k
views
Union of unaligned fastq reads
RNA-Seq
6.9 years ago by Jeffin Rockey ★ 1.3k
9
votes
2
replies
3.1k
views
GEOquery Problems to Get GEO dataset
Geoquery
8.1 years ago by Shicheng Guo ★ 9.4k
9
votes
10
replies
2.2k
views
[solved] Convert fold changes of multiple transcripts of a given gene to a single value characterising this gene
RNA-Seq
7.6 years ago by biostart ▴ 370
9
votes
10
replies
3.4k
views
generation of heat map by excel data.
R excel heatmap
updated 5.8 years ago by 43k • written 5.9 years ago by ▴ 10
9
votes
6
replies
1.3k
views
Genotype meaning
genotype BL21
2.8 years ago by A_heath ▴ 160
9
votes
7
replies
1.1k
views
ChIP-seq; investigate binding within region of tRNA genes
tRNA ChIP nf-core ChIP-seq
updated 23 months ago by 43k • written 24 months ago by ▴ 20
9
votes
6
replies
3.1k
views
Bug in JellyFish and DSK k-mer counting tool?
dsk jellyfish k-mer
7.4 years ago by scchess ▴ 640
9
votes
7
replies
5.4k
views
How to combine a different sources of pathway database (KEGG, BioCarta) for Pathway analysis.
Pathway enrichment analysis GWAS pathway analysis
7.8 years ago by kmsh410 ▴ 40
9
votes
9
replies
4.7k
views
ATAC-seq TSS profile plot interpretation
ATAC-seq TSS V-plot
4.4 years ago by nanoide ▴ 120
9
votes
16
replies
3.8k
views
6 follow
covert SAM to full length fasta
fasta SAM
updated 13 months ago by 43k • written 5.7 years ago by ▴ 710
9
votes
5
replies
479
views
Annotation of Complex Heatmap
complexheatmap
12 weeks ago by abiuma ▴ 30
9
votes
12
replies
1.5k
views
Copy number variations analysis
R CNV
updated 4.4 years ago by 11k • written 4.4 years ago by ▴ 70
9
votes
7
replies
1.3k
views
Reference genome location
reference positions FASTA alignment genome
updated 15 months ago by ★ 2.1k • written 15 months ago by • 0
9
votes
7
replies
2.4k
views
Merging BWT indices for BWA
BWA BWT read aligner merge
5.5 years ago by rgc255 ▴ 60
9
votes
4
replies
2.1k
views
[Code] Converte fasta/fa files to fastq
perl fastq sed fasta
updated 20 months ago by 43k • written 8.4 years ago by ★ 9.4k
9
votes
7
replies
2.7k
views
Averaging duplicates of a gene in RNA-Seq dataset
expression differential average R rna-seq
updated 2.8 years ago by ▴ 60 • written 2.8 years ago by ▴ 250
9
votes
7
replies
5.5k
views
fisher test with multiple samples
statistics
updated 2.4 years ago by 43k • written 9.8 years ago by ▴ 220
9
votes
13
replies
2.4k
views
single tumor vs multiple normal sample differential gene expression (RNA-Seq ) analysis using DESeq2
RNA-Seq DESeq2
updated 3.0 years ago by 43k • written 3.0 years ago by ▴ 30
9
votes
1
reply
6.1k
views
Why does MACS2 report multiple records for the same peak region?
ChIP-Seq macs macs2
updated 20 months ago by 43k • written 8.5 years ago by ★ 3.4k
9
votes
13
replies
15k
views
GC Content of Fasta file --- Python Help
sequence
7.2 years ago by Patrick Brennan ▴ 50
9
votes
16
replies
1.5k
views
I am trying to select some reference genome region of a bam file, but got an error
SAMTOOLS
updated 3.7 years ago by 15k • written 3.7 years ago by ▴ 160
9
votes
14
replies
3.1k
views
vcf to xls wrong columns
vcf
7.7 years ago by cristina_sabiers ▴ 110
9
votes
10
replies
2.5k
views
why there is 0/0 genotyp in VCF file?
VCF GATK Variant
4.7 years ago by star ▴ 350
9
votes
3
replies
7.2k
views
Statistical Distributions In Rna-Seq Data Analysis
statistics rna
updated 5.1 years ago by 20 • written 12.1 years ago by ▴ 380
9
votes
7
replies
2.1k
views
Sorting BLAST output files together?
blast
8.0 years ago by zgayk ▴ 90
1,000 results • Page 3 of 20
Recent Votes
Trimming sequences based on NCBI contamination screen report
warning[vg::giraffe]: Cannot cluster reads with a fragment distance smaller than read distance
Answer: Redirection of Duplicate PMIDs
Answer: How to convert plink files to Hapmap Format
Answer: How to convert plink files to Hapmap Format
Comment: Redirection of Duplicate PMIDs
Comment: Failed kmer content
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Recent Replies
Comment: How to convert plink files to Hapmap Format by bk11 ★ 2.3k
What type of phenotype is in your data? It looks like it does not have affection status (default values for affection status will be: 1 = u…
Comment: Redirection of Duplicate PMIDs by LauferVA 4.2k
Agree. This is also a great solution that flips the problem on its head, as it were, Dominick. I dont want to be preachy, but this is why i…
Answer: Redirection of Duplicate PMIDs by GenoMax 141k
Using [**EntrezDirect**][1] this may be much simpler if you have the grant number available. I tested this with a couple of random grants …
Answer: Redirection of Duplicate PMIDs by LauferVA 4.2k
Hi Dominick, One thing I am not sure of is, how is it that you got the other PMID in the first place? The reason I ask is that you mentio…
Comment: How to convert plink files to Hapmap Format by Sofia • 0
Thanks Marco, btw do you have any idea why I get this "Warning: Skipping --assoc/--model since less than two phenotypes are present." aft…
Comment: Subset Seurat object from Xenium spatial data by bk11 ★ 2.3k
For subsetting a sample, you can do something like this- Idents(seuratObj) <- "orig.ident" subj1 <- c("subject_1") subj1_seur…
Comment: Redirection of Duplicate PMIDs by LauferVA 4.2k
Ok! I have a recommendation. I'll submit it as an answer, pending your feedback. vincent
Comment: DYH17 Structure Prediction by anasjamshed ▴ 120
In modeller we need to use templates as well.so 63% is acceptable
Comment: DYH17 Structure Prediction by Ram 43k
Mensur said > The latter option assumes you know how to use Modeller Do you know how to use Modeller? I vaguely recall there being a mini…
Comment: Should I remove unlocalized scaffols in reference genome before alignment? by GenoMax 141k
OP is working with long reads so the chances of reads aligning to unlocalized scaffolds are relatively small. Doing some testing may be suf…
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks? by ATpoint 81k
I personally think that comparing the same peak between conditions is meaningful and comparing peaks within the same sample is not.
Comment: Should I remove unlocalized scaffols in reference genome before alignment? by ATpoint 81k
These regions are present in the genome and removing them might incorrectly redirect alignments to known genes. I don't see why you would r…
Comment: Should I remove unlocalized scaffols in reference genome before alignment? by njornet ▴ 20
Ok thank you! Do you know if there is an easy way of doing so with ncbi-genome-download or I need to use another tool?
Comment: Using vg gamsort with naive sorting algorithm by Pierre Lindenbaum 161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: Redirection of Duplicate PMIDs by dominickd • 0
The scope is all publications related to grants from an NIH award program. There are currently ~120k publications in total (about a few hun…
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