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121,908 results • Page 679 of 2439
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3
votes
1
reply
1.0k
views
How to download specific genomes
comparative ncbi genomes genomics assembly
updated 4.5 years ago by 153k • written 4.5 years ago by ▴ 30
0
votes
3
replies
2.3k
views
Network X used in Biopython
Biopython Graphs Python
4.5 years ago by anasjamshed ▴ 140
8
votes
6
replies
2.6k
views
How to select genes with multi-exon 3'UTR
rna-seq genome gff gene
updated 4.5 years ago by 9.3k • written 4.5 years ago by ▴ 190
1
vote
3
replies
1.1k
views
How to get DNA and RNA datasets from GEO,TCGA and EBI
dna-seq Genome rna-seq
4.5 years ago by Milan • 0
2
votes
2
replies
1.7k
views
How does e value for diamond blastx affects the result
analysis metagenomics genomics data
4.5 years ago by serene.s • 0
2
votes
1
reply
2.0k
views
Picard and GaTK HaplotypeCaller
gatk picard haplotypecaller duplicates
updated 4.5 years ago by ▴ 720 • written 4.5 years ago by • 0
0
votes
3
replies
1.6k
views
Generating an MDS plot in R for population stratification
R MDS Stratification PCA PLINK
4.4 years ago by nliberman • 0
3
votes
2
replies
5.7k
views
How to install PEER in R?
PEER R Rstudio RNA-Seq
4.5 years ago by sahar.salimi92 • 0
9
votes
5
replies
5.3k
views
tool for bam soft clipping reads within bed file regions
bam clipping bed
updated 3.2 years ago by 45k • written 9.6 years ago by ★ 3.6k
13
votes
14
replies
9.0k
views
8 follow
Limiting variant calls to amplicon target regions?
trimming alignment
updated 2.7 years ago by 45k • written 10.3 years ago by ▴ 10
1
vote
7
replies
4.3k
views
How to merge and average BedGraph files
bedtools terminal bg bedgraph
4.5 years ago by a_bis ▴ 40
2
votes
1
reply
957
views
Tool: Bioinformatics Programming Package
Package
updated 2.3 years ago by 45k • written 4.5 years ago by ▴ 10
0
votes
2
replies
1.3k
views
Can someone help me understand map and hap files
admixsim hap map
updated 2.5 years ago by 45k • written 4.5 years ago by • 0
0
votes
0
replies
1.4k
views
barplot for enrichment results
clusterProfile barplot RNAseq DESeq2
updated 4.5 years ago by 153k • written 4.5 years ago by • 0
2
votes
6
replies
2.1k
views
How can I retrieve nucleotide sequences from amino acid sequences?
nucleotide sequences protein
updated 4.5 years ago by 15k • written 4.5 years ago by ▴ 50
0
votes
3
replies
1.0k
views
Package to predict genomic variants from rna-seq read data
Genomics rna-seq
4.5 years ago by dk0319 ▴ 70
0
votes
1
reply
1.6k
views
Running Snakemake on the computing cluster
Snakemake HPC
updated 4.4 years ago by 45k • written 4.5 years ago by ▴ 340
0
votes
0
replies
794
views
Big difference in "free parameter" (np) in Sites Models for different models with CODEML (PAML)
Site-Models sequence PAML evolution CODEML
4.5 years ago by mauricio.1313 • 0
0
votes
1
reply
2.9k
views
use 16s rRNA data to predict metabolic pathway according to genome-scale network reconstructions
genome reconstruction metabolic
updated 4.5 years ago by • 0 • written 8.0 years ago by ▴ 60
1
vote
1
reply
1.3k
views
Extract MAF for vcf file
vcf MAF
updated 4.5 years ago by 166k • written 4.5 years ago by ▴ 10
3
votes
3
replies
1.4k
views
filtering a dataframe of DE GO terms with a dataframe containing GO terms of interest
GeneOntology
4.5 years ago by peter.berry5 ▴ 60
3
votes
2
replies
4.7k
views
How to fix error in Entrez-Direct: 429 Too Many Requests
Entrez-Direct
updated 19 months ago by 45k • written 4.5 years ago by ▴ 10
1
vote
2
replies
1.1k
views
SNP/Gene to cell type
cell SNPs
updated 2.3 years ago by 45k • written 4.5 years ago by ▴ 70
4
votes
2
replies
1.4k
views
Do FASTQ files from ArrayExpress already have adapter sequences trimmed?
adapters ArrayExpress
updated 4.5 years ago by 153k • written 4.5 years ago by ▴ 30
0
votes
3
replies
1.6k
views
Different files with SRA Explorer and SRA toolkit fasterq-dump
SRA_Explorer SRA-toolkit
updated 4.5 years ago by 153k • written 4.5 years ago by ▴ 110
0
votes
1
reply
1.1k
views
driver genes per sample or per group?
driver genes
updated 2.6 years ago by ▴ 940 • written 4.5 years ago by ▴ 60
45
votes
23
replies
7.5k
views
6 follow
Forum: biostar.slack.com: Chat for the biostars community -- [ feel free to join ]
chat slack
updated 2.6 years ago by 45k • written 7.5 years ago by 105k
0
votes
0
replies
1.1k
views
Interpretation of CNVkit output
gainloss tumor InterpretationOfResults CNVkit
4.5 years ago by Samiah ▴ 10
0
votes
0
replies
666
views
how to build a graph reference with HISAT-genotype
reference RNA-seq hisat2 alignment
4.5 years ago by minghuiguo448 • 0
2
votes
2
replies
1.2k
views
Convert protein name to letter e.g. p.Arg135Trp to p.R135W
aminoacid
updated 4.5 years ago by 21k • written 4.5 years ago by ▴ 60
0
votes
0
replies
1.4k
views
Will there be late amplification (ct value) for negative control in qPCR?
RNA QPCR cDNA
4.5 years ago by shail.nair05 ▴ 20
3
votes
7
replies
2.3k
views
7 follow
Annotation of non model fish (mahi mahi) genome
Assembly Annotation
updated 4.5 years ago by 9.3k • written 5.2 years ago by ▴ 90
2
votes
1
reply
1.2k
views
Building a biological database of coding sequence of Covid-19 with Python
python covid project database covid-19
updated 4.5 years ago by ▴ 940 • written 4.5 years ago by ▴ 10
1
vote
1
reply
1.0k
views
Argument "query". Incompatible with argument: `in_pssm' blast+
psiblast ncbi tblastn blast
4.5 years ago by rachid.fermi • 0
3
votes
2
replies
1.2k
views
What does BP stand for? | Reads and Assemblies
Macrogenomics read assembly
updated 2.5 years ago by 45k • written 4.5 years ago by ▴ 10
1
vote
3
replies
1.8k
views
"MethylKit" package for WGBS data
subjective
updated 4.5 years ago by ★ 3.1k • written 4.5 years ago by ▴ 40
1
vote
1
reply
979
views
gemBS aligner file format
gemBS aligner
updated 4.5 years ago by 153k • written 4.5 years ago by ▴ 40
0
votes
2
replies
1.2k
views
Samtools view error: header include @SQ line missing LN tag.
minimap2
updated 2.5 years ago by 45k • written 4.5 years ago by • 0
3
votes
1
reply
1.5k
views
Calling TE sequences from VCF files
next-gen variant-calling sniffles
updated 23 months ago by 45k • written 5.8 years ago by ▴ 210
1
vote
2
replies
1.4k
views
How to choose the best alignment from mapping with bowtie2?
alignment bowtie2 sequence
4.5 years ago by anikcropscience ▴ 270
20
votes
8
replies
2.6k
views
9 follow
Forum: What are some major historic shifts in bioinformatic methodologies?
meta history
updated 4.5 years ago by 15k • written 4.5 years ago by 23k
0
votes
0
replies
600
views
Experimental/Biological datasets for Gene Regulatory Network Reconstruction
Gene network data Regulatory microarray Network
4.5 years ago by Anjali Setiya • 0
2
votes
4
replies
3.1k
views
Where can I find a fasta for mitochondrial genes?
mitochondrial genes
updated 4.5 years ago by 14k • written 4.5 years ago by ▴ 280
0
votes
1
reply
1.3k
views
Where to download raw counts (RNAseq) and breakpoints coordinates (cancer related) for testing?
RNAseq cancer
updated 2.5 years ago by 45k • written 4.5 years ago by ★ 1.3k
2
votes
2
replies
2.3k
views
Interpretation of functional prediction pathogenicity scores regarding variants with multiple transcripts in ANNOVAR
annovar pathogenicity cancer CADD
4.5 years ago by svlachavas ▴ 790
4
votes
2
replies
1.6k
views
SNP‐based enrichment analysis for WGCNA modules using an hypergeometric test
hypergeometrictest SNPs WGCNA
4.5 years ago by andres.firrincieli 3.9k
2
votes
5
replies
2.7k
views
MUtect2-Vardict
Mutect2 VarDict NGS
updated 4.4 years ago by 89k • written 4.5 years ago by ▴ 20
2
votes
2
replies
1.8k
views
featureCounts outputs zero raw read counts!!
featureCounts DGE
updated 4.5 years ago by 153k • written 4.5 years ago by ▴ 10
1
vote
4
replies
2.0k
views
CNA figure
python figure plot R CNA
updated 4.5 years ago by 89k • written 4.5 years ago by ▴ 10
0
votes
3
replies
1.3k
views
Genome assembly
assemblies Genome
updated 4.5 years ago by 153k • written 4.5 years ago by ▴ 10
121,908 results • Page 679 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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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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