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1,000 results • Page 3 of 20
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10
votes
15
replies
6.1k
views
DIAMOND blast imported into MEGAN6 has no taxonomic assignment
blast MEGAN6 Taxonomy DIAMOND
7.4 years ago by Farbod ★ 3.4k
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
2
replies
596
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
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
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
8
replies
2.3k
views
Blast scores...two annotations for the same piece of sequence
alignment
updated 22 months ago by 43k • written 9.1 years ago by ▴ 50
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
7.1 years ago by Vasu ▴ 770
10
votes
10
replies
3.8k
views
Parameter optimization STAR
RNA-Seq
6.2 years ago by XBria ▴ 90
9
votes
13
replies
3.3k
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 10.7 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
11
replies
1.5k
views
6 follow
Split up excel cell into multiple records
excel byonic
6.8 years ago by rshipman ▴ 30
9
votes
10
replies
2.8k
views
About GATK4 Mutect2 runtime (Whole Exome seq)
GATK Whole Exome Sequencing Mutect2
3.2 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
5.4 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
4.2 years ago by schlogl ▴ 160
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 5.8 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
10
replies
1.8k
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
15
replies
1.3k
views
Construction of single sequence assembly out of contigs
Contigs Bacteria Genome WGS
4 months ago by analyst ▴ 20
9
votes
12
replies
1.4k
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
1.2k
views
Reference genome location
reference positions FASTA alignment genome
updated 15 months ago by ★ 2.1k • written 15 months ago by • 0
9
votes
6
replies
3.4k
views
SOAPaligner 2.21 - does it replace all Ns by Gs in reads?
Soapaligner alignment
updated 2.5 years ago by 43k • written 9.9 years ago by 8.3k
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
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
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
8
replies
1.7k
views
Union of unaligned fastq reads
RNA-Seq
6.8 years ago by Jeffin Rockey ★ 1.3k
9
votes
13
replies
15k
views
GC Content of Fasta file --- Python Help
sequence
7.2 years ago by Patrick Brennan ▴ 50
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
5
replies
711
views
Prophage prediction tool
prophage PHASTER prediction
updated 9 months ago by 141k • written 9 months ago by ▴ 160
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
27
replies
7.5k
views
How do I use Glimmer 3.02?
sequencing
updated 5.2 years ago by • 0 • written 6.1 years ago by ▴ 50
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
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
7
replies
2.1k
views
Sorting BLAST output files together?
blast
8.0 years ago by zgayk ▴ 90
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
11
replies
6.6k
views
microRNA Illumina Sequencing - Very low alignment rate
sequencing Assembly RNA-Seq
updated 2.2 years ago by 43k • written 9.7 years ago by ▴ 90
9
votes
7
replies
5.3k
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
14
replies
4.3k
views
Explanation on Paired end single index for RNA seq
RNA-Seq
updated 2.0 years ago by 43k • written 9.2 years ago by ▴ 70
9
votes
14
replies
3.1k
views
vcf to xls wrong columns
vcf
7.7 years ago by cristina_sabiers ▴ 110
9
votes
2
replies
572
views
Answer needed urgently
Deep
updated 19 months ago by ★ 27k • written 19 months ago by • 0
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
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
1,000 results • Page 3 of 20
Recent Votes
Installing/switching between versions of R/Rstudio/Bioconductor
How To Generate Phylogeny Tree, Based On Snps?
How To Construct Phylogenetic Tree Using Snps
Basic normalization, batch correction and visualization of RNA-seq data
A: Read counts of STAR with gff file
Comment: Free/open source 23andme-like analysis
A: How to obtain all accession.version identifiers for a BLAST database using ENTRE
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Recent Replies
Comment: Memory usage of picard Samsort by ATpoint 81k
Guys, just use `samtools sort` which won't get you into trouble with any of that.
Comment: Ciriquant not configuring hisat2 indexed files by Carlo Yague 8.6k
I don't know for sure, but I think that decreasing the amount of threads (1 or 2 instead of 4) will decrease the memory requirements of the…
Answer: Memory usage of picard Samsort by tamas.malkocs • 0
For me, setting `TMP_DIR` (`--TMP_DIR /home/tmp`) didn't work in picard 2.21.1. What solved the issue was setting the environmental variabl…
Answer: Plink merge errors. by Dinmukhamed • 0
I found answer https://www.biostars.org/p/101191/.
Comment: Ciriquant not configuring hisat2 indexed files by Atul K. • 0
it worked. Thank you. Now my terminal is crashing, seems 16gb of RAM and 4 cores isn't enough. Can you suggest something?
Comment: Adding CB tag to bam file by Maria • 0
I checked Picard ```AddOrReplaceReadsGroups``` and ```AddOATag```. Is that what you're referring to?
Comment: Free/open source 23andme-like analysis by Michael 54k
Noted that 'accurate' wasn't among your criteria ;) Anyway, most variant callers are free open-source software. However, for ancestry ana…
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi by Pierre Lindenbaum 161k
> server so I cannot use Blat for this purpose. blat is avilable as a standane tool: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86…
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi by b.contreras.moreira ▴ 160
My favourite for this task would be [GMAP]( http://research-pub.gene.com/gmap ), which can produce GFF format with option `-f 2`. It is…
Answer: Prediction of Ribosomal RNA Genes Using RNAmmer Software by colindaven 6.3k
Another alternative is the truly free implementation barrnap https://github.com/tseemann/barrnap. This is also installable via conda so qui…
Comment: Filtration Of Reads With Length Lower Than 30 From Bam by Hagen ▴ 10
thanks! This saved me quite some time, I was about to write code to calculate the aligned length from the CIGAR. But this can be done with …
Comment: Per base sequence content failed miserably by Kai Xin • 0
will look into that. Thank you very much
Comment: Korean human genome reference file by SeoGyun • 0
Thanks..... But I want to do imputation, so I have to make it as a vcf file, but the site only has a fatsa file....
Comment: miRNAs quantification using mirdeep2 tool by Ashok • 0
thank you for your reply https://github.com/rajewsky-lab/mirdeep2/blob/master/TUTORIAL.md i saw this github tutorial for miRNA quantifica…
Comment: Load a full GFF3 into annotation track using arrow (Apollo) by cmdcolin ★ 3.8k
Hi there, I let a developer know of this thread and they said they can check it out next week. Feel free to post to the https://github.com/…
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