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Forum: Opinions on SLAM-Seq for Differential Gene Analysis
DGE RNA-Seq htseq
updated 4.3 years ago by ★ 7.7k • written 4.3 years ago by ▴ 70
1
vote
2
replies
1.7k
views
Basic questions about SPAdes, metaSPAdes
metaspades
4.3 years ago by yingcraft • 0
0
votes
3
replies
4.5k
views
Questions on ssGSEA
RNA-seq gsva ssGSEA alignment
updated 4.3 years ago by ▴ 90 • written 4.3 years ago by ▴ 80
0
votes
1
reply
701
views
.bam .sam paired or unique aligment
aligment sam bam
updated 2.5 years ago by 45k • written 4.3 years ago by • 0
6
votes
3
replies
1.5k
views
Tool for Protein Alignment/Superimposition
protein superimposition alignment
4.3 years ago by antoniaa ▴ 30
1
vote
3
replies
1.3k
views
Cannot great a gene by gene matrix in Rstudio
gene matrix
updated 2.8 years ago by 45k • written 4.3 years ago by • 0
6
votes
10
replies
2.2k
views
what does very low estimates but a significant P value mean.
coefficients pvalue regression
updated 4.2 years ago by ★ 3.1k • written 4.3 years ago by ▴ 10
1
vote
1
reply
1.4k
views
How can I compare the similarities of two transcriptomes?
transcriptome similarity rnaseq
updated 4.3 years ago by ★ 1.1k • written 4.3 years ago by ▴ 30
4
votes
6
replies
8.3k
views
calculate ti/tv ratio in WGS data
sequencing ti/tv ratio
updated 4.3 years ago by • 0 • written 7.4 years ago by ▴ 10
0
votes
1
reply
851
views
what is the length of sliding window in trimming options how to get it
fastq fasta SRA
updated 2.5 years ago by 45k • written 4.3 years ago by ▴ 20
1
vote
1
reply
2.5k
views
RNA-seq gene list - HOMER Gene based analysis
RNA-Seq homer
updated 4.3 years ago by ▴ 370 • written 8.2 years ago by ▴ 20
3
votes
4
replies
1.9k
views
Duplicate ID error with update-name flag
Chromosome SNP position Plink unix rsid
updated 4.3 years ago by 12k • written 4.3 years ago by ▴ 20
0
votes
1
reply
1.1k
views
Generating multiple species consensus alignments for tree topology tests
bcftools alignment fasta iqtree vcf
updated 4.3 years ago by ▴ 160 • written 4.3 years ago by ▴ 40
1
vote
8
replies
2.1k
views
How to map rsIDs to KEGG variant Ids
dbsnp kegg rsid
4.3 years ago by david.f.stein ▴ 10
0
votes
1
reply
998
views
blastn cut off values
blast
updated 4.3 years ago by ▴ 160 • written 4.3 years ago by ▴ 50
2
votes
1
reply
5.4k
views
vcftools and SnpSift give different values for Ts/Tv ratio
variant SNP vcf transversion transition
updated 3.9 years ago by 45k • written 10.6 years ago by ▴ 380
13
votes
6
replies
11k
views
6 follow
convert sam into paf format
genome alignment sequencing assembly SNP
updated 2.7 years ago by ▴ 30 • written 4.8 years ago by ▴ 10
0
votes
4
replies
1.3k
views
add text to a path by adding text to it with python (FTP Path NCBI)
python ncbi pandas
4.3 years ago by Debut ▴ 20
1
vote
0
replies
895
views
Job: Opportunity: Bioinformatics Software Engineer - Bioinformatics Core @ Memorial Sloan Kettering Cancer Center, New York, NY (US)
cancer_biology Python R
updated 4.2 years ago by 45k • written 4.3 years ago by ▴ 10
0
votes
1
reply
785
views
Differential Expression Analysis Using RPKM
RPKM RNA-seq DE
updated 4.3 years ago by 15k • written 4.3 years ago by • 0
1
vote
1
reply
1000
views
Single cell clusters annotating to same cell-type
Monocle Single-cell Seurat Pseudotime
updated 4.3 years ago by ★ 1.1k • written 4.3 years ago by ▴ 50
0
votes
2
replies
1.2k
views
Exact duplicated reads between independent replicates
ChIP NGS low-input duplicates Illumina
4.3 years ago by Miguel • 0
0
votes
1
reply
1.9k
views
Surat object UMAP - highlight cells based on Citeseq data
Seurat UMAP
updated 4.3 years ago by 3.4k • written 4.3 years ago by ▴ 40
2
votes
1
reply
1.0k
views
Obtaining all independent SNPs
SNPs permutation pruning clumping PLINK
updated 4.3 years ago by ★ 4.8k • written 4.3 years ago by ▴ 10
1
vote
2
replies
1.2k
views
Cytoscape for co-occurence network analysis
Microbiome 16S analysis Cytoscape Network
4.3 years ago by Bioinfonext ▴ 470
3
votes
2
replies
2.2k
views
Structural variants calling in a population
structural variants
updated 4.3 years ago by • 0 • written 8.3 years ago by ★ 1.0k
5
votes
4
replies
7.2k
views
Merge vcf files of structural variants
structural_variants vcf merge
updated 4.3 years ago by • 0 • written 7.1 years ago by ▴ 20
3
votes
2
replies
4.2k
views
For loop to parallel run commands
Unix bash Linux
4.3 years ago by endretoth ▴ 40
19
votes
13
replies
9.7k
views
8 follow
Error installing bcl2fastq 2.20 in make step - Ubuntu 18.04
software error bcl2fastq ubuntu
updated 2.7 years ago by • 0 • written 6.2 years ago by ▴ 140
0
votes
2
replies
792
views
Pseudogenes identification and removal from BRCA samples
NGS
4.3 years ago by smrutimayipanda ▴ 20
0
votes
3
replies
1.0k
views
very low number of reads aligned in bowtie (colourspace)
map colourspace bowtie
updated 4.3 years ago by 153k • written 4.3 years ago by ★ 1.3k
1
vote
1
reply
779
views
Multiple genes comparison
Transcriptome RNA-seq
updated 4.3 years ago by ▴ 160 • written 4.3 years ago by ▴ 10
0
votes
2
replies
1.2k
views
Tools for SNPs and Indels (RNA seq. Nanopore)
Indel RNA-Seq SNP Nanopore
updated 2.5 years ago by 45k • written 4.3 years ago by ▴ 30
4
votes
3
replies
1.8k
views
Complex DESeq2 sample file set up
complex design DESEq2 RNAseq
4.2 years ago by rva_jango ▴ 10
0
votes
0
replies
823
views
Job: Bioinformatician at the Institute of Botany, Czech Academy of Sciences
polyploidization diversification plant
updated 4.2 years ago by 45k • written 4.3 years ago by • 0
0
votes
3
replies
1.3k
views
DESeq2: Variable Importance
DESeq2
updated 4.3 years ago by 89k • written 4.3 years ago by ▴ 30
1
vote
6
replies
2.0k
views
Is BLASTp the quickest method to get a rough idea on ortholog from protein sequence?
blastp ortholog homolog blast
updated 4.3 years ago by 15k • written 4.3 years ago by ▴ 190
0
votes
0
replies
526
views
GOstat error : No results met the specified criteria
RNAseq GO gostat
4.3 years ago by ryme ▴ 30
4
votes
2
replies
1.1k
views
Remote access- data security
Remote-Access
updated 4.3 years ago by ★ 3.4k • written 4.3 years ago by ▴ 110
1
vote
1
reply
1.3k
views
Imputation with Beagle 5.2 for whole exome data at once
Beagle Imputation
updated 4.3 years ago by 2.9k • written 4.3 years ago by ▴ 10
0
votes
2
replies
1.4k
views
Pedigree file for 1k genome , build 38
build 1000G pca 38
4.3 years ago by AVA ▴ 40
5
votes
3
replies
1.4k
views
Why is NNN sequence at the end of chromosomes
Telomere sequence NNN
4.3 years ago by cammm988 ▴ 10
1
vote
1
reply
1.1k
views
How to calculate the *necessary* sequencing depth for a SNP
sequencing SNP analysis depth statistics Sequencing
updated 4.3 years ago by ▴ 720 • written 4.3 years ago by • 0
0
votes
1
reply
774
views
Change genbank files orientation to '5 > '3 based on their ORF direction
reverse genbank ORF complete
updated 4.3 years ago by 22k • written 4.3 years ago by ▴ 10
3
votes
9
replies
2.4k
views
Alternative polyadenylation detection from short-read RNA-seq, software suggestions
software apa alternative-polyadenylation
4.3 years ago by Gregor Rot ▴ 550
2
votes
4
replies
2.3k
views
KRAKEN2 database build ref-seq have some missing data
KRAKEN2 ref-seq
4.2 years ago by jimmy0958073736 ▴ 40
1
vote
4
replies
1.1k
views
How to verify the authenticity of the data set downloaded from database?
data analysis
4.3 years ago by 465336766 • 0
1
vote
6
replies
4.2k
views
bcftools plugin fill-tags with functions
AVG fill-tags bcftools
4.2 years ago by diana.cornejo • 0
3
votes
4
replies
1.8k
views
Duplicate results in vardict vcf
vardict
updated 4.3 years ago by 45k • written 4.3 years ago by ▴ 60
6
votes
4
replies
2.8k
views
Unable to install EnhancedVolcano: non-zero exit status
Harfbuzz EnhancedVolcano R
updated 4.3 years ago by 89k • written 4.3 years ago by ▴ 90
121,903 results • Page 634 of 2439
Recent Votes
Answer: Tried building a compact sequence format with 4-bit storage
Tried building a compact sequence format with 4-bit storage
Shift in RNA 3' position, Term-Seq vs RNASeq
Comment: STARlong for pacbio Isoseq reads
Comment: Automatically annotating a feature using a genbank file
Answer: Is this PCA plot correct??
Answer: Is this PCA plot correct??
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Recent Replies
Comment: Is total miRNA in EV constant? Implications for library size normalization. by Gordon Smyth ★ 8.3k
RNA-seq is very good at relative analyes. It would be straightforward to determine which miRNAs are relatively more abundant, compared to o…
Comment: Tried building a compact sequence format with 4-bit storage by Pranava ▴ 10
Woah!!! Thank you very much, Matthias. I honestly didn't even know some of those existed and I will definitely go through them and try to u…
Answer: Tried building a compact sequence format with 4-bit storage by Matthias Zepper 5.1k
Hello Pranava, Thanks for sharing your repository. Devising a new file format is an interesting undertaking and certainly a task with many…
Answer: Gene Ontology Enrichment with LOC gene IDs in Common Carp (Cyprinus carpio) by GenoMax 153k
`LOC` gene ID's are often assigned to uncharacterized genes and you may not get useful information from databases for them, thus they will …
Comment: Whole Genome Sequencing IG regions by GenoMax 153k
> are the calls I am seeing reliable or should I take them with something of a pinch of salt? Not sure what calls you are referring to but…
Comment: RNA-SEQ where only a subset of genes is of interest by piffelpaff • 0
Sorry to revive this ancient thread but I'm currently discussing the same question with some people in my lab and would love to somebody po…
Answer: STARlong for pacbio Isoseq reads by YuZJ • 0
Hello, you may try deSALT (DOI: 10.1186/s13059-019-1895-9, GitHub: ydLiu-HIT/deSALT) or uLTRA (DOI: 10.1093/bioinformatics/btab540, GitHub:…
Comment: Shift in RNA 3' position, Term-Seq vs RNASeq by acvill ▴ 350
Without knowing the details of the Term-seq method, could the 38 nt shift be accounted for by the difference in the position of the ribosom…
Comment: STARlong for pacbio Isoseq reads by Buffo ★ 2.4k
Thanks, I'll give it a try.
Comment: STARlong for pacbio Isoseq reads by GenoMax 153k
You could give `mapPacBio.sh` from BBMap suite a try while you wait for other answers. That works for reads up to 6 kb. BBMap has a new hom…
Comment: STARlong for pacbio Isoseq reads by Buffo ★ 2.4k
The average is 1.8kb. I was planning to post it on GitHub, but it seems like the repository has been unattended for the last months, so I d…
Comment: Getting just fastqc.zip file? by GenoMax 153k
Yes, You can either use it on command line or use the graphical user interface.
Comment: STARlong for pacbio Isoseq reads by GenoMax 153k
What is the average length of your reads? That error sounds like a bug, so you may want to post that on `STAR` repo as an issue. I assume …
Comment: Getting just fastqc.zip file? by pourhangleila95 • 0
I want to perform fastQC on my data.Do you use fastQC software for doing it?
Comment: Whole Genome Sequencing IG regions by 719 • 0
Sorry for the poor wording of the original post, also should say I really appreciate people taking a moment to look at my post. My main con…
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