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121,907 results • Page 680 of 2439
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2
votes
1
reply
2.2k
views
draw and display a Venn diagram with up to 7 sets.
Venn
updated 4.5 years ago by 10k • written 4.5 years ago by ▴ 80
0
votes
0
replies
891
views
Job: Postdoc position in non-coding RNA biology and bioinformatics
lncRNA miRNA Postdoc RNA
updated 4.2 years ago by 45k • written 4.5 years ago by • 0
0
votes
0
replies
976
views
Pathway enrichment analysis vs GSEA for single cell RNA sequencing data analysis
GSEA pathway scRNAseq
4.5 years ago by aa123 • 0
0
votes
1
reply
864
views
Patient-derived omics data with psychiatric illness scores like PANSS score
mentalillness omicsdata score
updated 4.5 years ago by 89k • written 4.5 years ago by • 0
4
votes
3
replies
6.2k
views
Getting all gene members in a Reactome Pathway
Reactome Bioconductor
updated 4.5 years ago by ▴ 580 • written 6.2 years ago by ▴ 180
0
votes
1
reply
1.4k
views
Reactome reaction enumeration with DefinedSets
reactome
updated 4.5 years ago by ▴ 580 • written 5.9 years ago by ▴ 10
1
vote
2
replies
2.2k
views
Why is mapper.pl from mirdeep2 producing an empty mapping file?
mirna ngs next-gen
updated 4.5 years ago by ▴ 10 • written 4.8 years ago by ▴ 300
0
votes
2
replies
1.5k
views
Replace Drugbank IDs with Drug name [R]
r dictionary drugbank
updated 4.5 years ago by 13k • written 4.5 years ago by • 0
10
votes
15
replies
6.0k
views
conda install -c bioconda simlord | SimLoRD
ubuntu bash SimLoRD reads fastq
4.5 years ago by Anonymous ▴ 10
0
votes
3
replies
9.8k
views
R: exporting summary of coxph object
R Cox regression data export
updated 4.5 years ago by • 0 • written 9.1 years ago by ▴ 230
8
votes
3
replies
3.9k
views
Create duplicate columns in R for a large data frame
R dataframe
updated 4.5 years ago by 21k • written 4.5 years ago by ▴ 280
2
votes
2
replies
1.7k
views
TCGABioLinks getManifest() function. How to alter saved file name?
TCGA R Bioconductor
updated 4.5 years ago by ▴ 10 • written 4.7 years ago by • 0
2
votes
6
replies
2.2k
views
A mismatch between DiffBind's results and the same results retreieved as DESeq2 (from DiffBind)
DiffBind
updated 4.5 years ago by ★ 19k • written 4.5 years ago by ▴ 390
7
votes
3
replies
2.1k
views
Unable to match Ensembl IDs from TCGA-related CNV datasets
Ensembl Number TCGA TCGABiolinks Variation Copy
updated 4.5 years ago by 89k • written 4.5 years ago by ▴ 20
1
vote
1
reply
936
views
How to find the taxonomic position of E.coli
ecoli
updated 2.5 years ago by 45k • written 4.5 years ago by • 0
1
vote
4
replies
1.7k
views
How to select the reads with a certain adapter in a fastq file in R
SmartSeq R Bioconductor Shortre RNAseq
updated 4.5 years ago by 89k • written 4.5 years ago by • 0
0
votes
0
replies
1.1k
views
AXT format
sequence alignment multiple mafft
4.5 years ago by Rahul ▴ 30
0
votes
4
replies
2.2k
views
Replace headers of fasta while with simplified headers from another file
python fasta bash
updated 4.5 years ago by 21k • written 4.5 years ago by • 0
0
votes
1
reply
1.4k
views
Blast a CDD PSSM against a genome
pssm CDD blast
updated 4.5 years ago by ★ 30k • written 4.5 years ago by ▴ 270
0
votes
1
reply
959
views
Can the odds ratio change based on a multiple logistic regression model?
statistics
updated 4.5 years ago by 13k • written 4.5 years ago by • 0
0
votes
1
reply
1.8k
views
Seurat: Any way to identify genes expressed only in one condition of one cluster?
scRNAseq Seurat
updated 4.5 years ago by ★ 19k • written 4.5 years ago by • 0
1
vote
10
replies
3.8k
views
Trimming customed adaptor sequences with trimmomatic
trimmomatic trim illumina exon
updated 4.2 years ago by 45k • written 4.5 years ago by ▴ 80
9
votes
11
replies
4.7k
views
Bash loop for bbduk
bash bbduk
updated 4.5 years ago by 21k • written 4.5 years ago by ▴ 30
0
votes
0
replies
1.1k
views
HybPiper Error
HybPiper phylogeny
updated 2.8 years ago by 45k • written 4.5 years ago by ▴ 80
3
votes
4
replies
4.0k
views
PRS using PGS Catalog
PRS PGS polygenic PRSice
updated 4.0 years ago by ★ 4.8k • written 4.5 years ago by ▴ 10
0
votes
1
reply
1.5k
views
How to convert an RDS file containing annotated cells to a loom file
R Scanpy RNA-seq
updated 4.5 years ago by 13k • written 4.5 years ago by • 0
0
votes
3
replies
1.8k
views
Use of ISCN in public knowledgebases
sequence
updated 4.5 years ago by • 0 • written 8.3 years ago by ▴ 100
4
votes
4
replies
1.3k
views
How to get started with transcriptome sequencing as a bioinformatics beginner.
transcriptome
updated 2.5 years ago by 45k • written 4.5 years ago by • 0
0
votes
0
replies
821
views
Plot only the genome-wide trans contacts in a Hi-C matrix (no cis contacts)
juicer Hi-C inter-chromosomal cooler trans
4.5 years ago by kalavattam ▴ 380
1
vote
10
replies
2.3k
views
How to remove these a subset fasta file
orfipy
updated 4.5 years ago by 45k • written 4.5 years ago by ▴ 10
7
votes
7
replies
26k
views
Calculating fpkm from raw counts
RNA-Seq R fpkm
updated 4.0 years ago by ▴ 10 • written 7.4 years ago by ▴ 260
0
votes
2
replies
2.2k
views
How to calculate frequency of heterozygous SNPs in multisample VCF file and to filter out over a specific range?
bcftools vcftools
4.5 years ago by kumar.vinod81 ▴ 340
3
votes
7
replies
2.8k
views
How to add gene function/protein name, start and end position to DESeq2 results for bacteria
deseq2 annotation
updated 4.5 years ago by 56k • written 4.5 years ago by • 0
1
vote
0
replies
1.8k
views
Job: Software Developer: EB-Environ Genomics & Systems Bio
JSON-Schema LinkML Python UML
updated 2.5 years ago by 45k • written 4.5 years ago by ▴ 70
4
votes
2
replies
4.2k
views
Trouble downloading files with fasterq-dump
sratoolkit
4.5 years ago by Rogerio Ribeiro ▴ 110
0
votes
0
replies
2.2k
views
Job: Postdoc position in microbiome gut-brain neuroscience @ Singapore A*STAR NTU ; 新加坡科技研究局南洋理工大学医学院诚聘博士后
neuroscience behavior microbiome
updated 4.2 years ago by 45k • written 4.5 years ago by • 0
0
votes
0
replies
661
views
using RNAseq reads to verify predicted gene models
prediction gene RNA-seq
4.5 years ago by sullis02 ▴ 40
3
votes
3
replies
2.1k
views
Simulate 100 Reads from .fastq file | FASTQC
fastq FASTQC Linux
updated 18 months ago by 45k • written 4.5 years ago by ▴ 10
1
vote
2
replies
1.3k
views
CDS regions of a gene
coding regions CDS two sequences FASTA
4.5 years ago by ali.al-fatlawi ▴ 10
3
votes
7
replies
5.5k
views
bash: sudo: command not found | ea-utils installation [CLOSED]
fastq ea-utils reads bash linux
4.5 years ago by Anonymous ▴ 10
0
votes
0
replies
936
views
Parsing a bed file to vcf file in Python
python3.8 python
4.5 years ago by alex_gon87 • 0
0
votes
0
replies
647
views
Hosting scRNA-seq data for query
Shiny Seurat scRNA-seq
4.5 years ago by LacquerHed ▴ 30
0
votes
0
replies
776
views
Comparison of ChIP-seq tracks from two cell lines using FC over control (ENCODE data)
ChIP-seq H3K27ac bigWig ENCODE
4.5 years ago by erica.fary ▴ 20
9
votes
9
replies
4.4k
views
Where can I lookup old merged rsIDs?
SNP
updated 4.5 years ago by ▴ 80 • written 8.6 years ago by ▴ 150
0
votes
1
reply
966
views
BlastN - Optimal recipocal blast command line options ?
alignment blastn
updated 4.5 years ago by 15k • written 4.5 years ago by ▴ 1000
3
votes
4
replies
2.7k
views
bash: conda: command not found | for SimLord [CLOSED]
windows bash simlord miniconda
updated 4.5 years ago by 153k • written 4.5 years ago by ▴ 10
0
votes
11
replies
7.4k
views
Extracting reads from one barcode in a bam file
extract bam barcode
4.5 years ago by msrinivasan • 0
0
votes
1
reply
1.0k
views
How to make factor level dynamic input field in shiny dashboard
flexdashboard shinydashboard shiny
updated 4.5 years ago by 89k • written 4.5 years ago by ▴ 20
1
vote
5
replies
6.4k
views
Multiple Psi-Blast Iterations From Command Line Using Remote Database
blast pssm
updated 4.3 years ago by ▴ 90 • written 12.7 years ago by ▴ 10
1
vote
6
replies
3.3k
views
Dealing with chimeric assembly contigs
comperative-genomics assembly chimera-contig
updated 4.5 years ago by ▴ 600 • written 4.5 years ago by ▴ 70
121,907 results • Page 680 of 2439
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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: Hifiasm is getting killed while trying to assemble a genome by Panos ★ 1.8k
Why don't you subsample your HiFi reads and try running hifiasm again? Maybe this will help if you have memory problems. However, I haven't…
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?
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