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121,908 results • Page 42 of 2439
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316
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Converting map & ped files to binary file. Missing info
Map Ped plink
updated 8 months ago by 45k • written 8 months ago by • 0
0
votes
2
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1.9k
views
Error in .Call2("C_solve_user_SEW", refwidths, start, end, width, translate.negative.coord
maftools
updated 8 months ago by ▴ 50 • written 2.3 years ago by ▴ 40
1
vote
3
replies
670
views
Is there a way or a tool to compare two hmm DNA profiles?
biotool hmmprofile hmm-hmm
8 months ago by abarcajose97 • 0
5
votes
2
replies
858
views
LASSO regression for gene selection and clinical variables
LASSO feature classification selection edgeR
updated 8 months ago by ★ 30k • written 8 months ago by ▴ 10
0
votes
4
replies
989
views
How to Check the Quality of a .fasta File for Sequence Alignment?
sequence-alignment fasta quality-control
updated 8 months ago by 7.9k • written 8 months ago by • 0
0
votes
3
replies
688
views
Kmerfinder database with bacteria, archea, and eukaryotic data
kmer
updated 8 months ago by 15k • written 8 months ago by ▴ 60
5
votes
5
replies
822
views
rna-seq reads not passing fastqc
rna-seq fastqc
8 months ago by Luna • 0
3
votes
6
replies
1.0k
views
Is there a proper way to choose bins in barplot
visualization plot bar
8 months ago by QX ▴ 80
1
vote
1
reply
630
views
Seeking advice for a machine learning project with RNA-seq data
ML gene_expression machine_learning DGE deep_learning
updated 8 months ago by ★ 3.1k • written 8 months ago by ▴ 10
0
votes
0
replies
366
views
Search and return transcript types from gene symbols by querying mygene.info or ensembl rest APIs
Gene Ensembl MyGene Transcriptomics Identification
8 months ago by m.musgrove • 0
0
votes
0
replies
460
views
Questions about genome annotation of non-coding RNA with infernal
ncRNA annotation
8 months ago by Abieskawa • 0
3
votes
1
reply
591
views
samtools tview special character
samtools bam rna
updated 8 months ago by 166k • written 8 months ago by ▴ 250
0
votes
2
replies
862
views
snpEff 'java.lang.OutOfMemoryError: Java heap space' problem despite increasing initial and maximum heap size to 10g and 20g respectively
heapsize conda snpeff anaconda java
updated 8 months ago by 7.9k • written 8 months ago by • 0
0
votes
6
replies
1.1k
views
Convert miRNA_ID to GENE-symbol
Gene_Symbol
updated 8 months ago by 22k • written 8 months ago by • 0
1
vote
0
replies
918
views
Job: A 2 year postdoc position: The Genetics of the Silk Road
Postdoc ancientDNA paleogenetics SilkRoad AI
8 months ago by eranelhaik ▴ 30
0
votes
1
reply
436
views
scRNA-seq analysis after overexpressing a specific gene
overexpression scRNA-seq
updated 8 months ago by ★ 1.6k • written 8 months ago by ▴ 10
0
votes
3
replies
630
views
SCRNA calculate the average expression
SCRNA cell-single-sequence
updated 8 months ago by ★ 1.6k • written 8 months ago by ▴ 30
2
votes
1
reply
529
views
Degree of Freedom Settings in edgeR limma
degree freedom voom analysis differential of edgeR limma
updated 8 months ago by 89k • written 8 months ago by • 0
0
votes
0
replies
330
views
Convert genepop to bayescan format
RAD-seq bayescan genepop pgdspider stacks
updated 8 months ago by 153k • written 8 months ago by • 0
2
votes
3
replies
669
views
missing data in taxonomy
taxonomy ncbi
8 months ago by noodle ▴ 650
3
votes
3
replies
1.0k
views
NA12878, NA12891 and NA12892 gold standard samples information
standard gold variant BAM calling
updated 8 months ago by 153k • written 8 months ago by ▴ 10
0
votes
0
replies
311
views
AA/AB/BB Genotype information to Numeric
genotype illumina SNP
8 months ago by Emilie ▴ 10
0
votes
2
replies
690
views
Merge paired end reads after mapping in BAM files
bam paired-end merge
updated 8 months ago by ★ 1.6k • written 8 months ago by • 0
0
votes
0
replies
351
views
How to perform cross-species integration?
Integration Seurat single-cell scrna-seq
8 months ago by Shankar112 • 0
6
votes
9
replies
1.4k
views
Unexpected spliced/unspliced percentages in scRNA-seq data
seq Spliced unspliced analysis velocity data scRNA
updated 8 months ago by ★ 2.1k • written 8 months ago by ▴ 10
0
votes
2
replies
626
views
Spliced and unspliced counts from HIVE scRNA-seq data
hive velocyto scvelo scrna-seq
8 months ago by anna_o • 0
1
vote
1
reply
591
views
Whole genome resequencing sample size for population genetics?
whole_genome_resequencing population_genetics
updated 8 months ago by ★ 3.1k • written 8 months ago by • 0
0
votes
1
reply
1.0k
views
Job: Post-doctoral Research Fellow Level 1
Biomedical Researcher Post-doc Biomolecular
8 months ago by jagoda.wychowaniak • 0
7
votes
14
replies
1.9k
views
Proteomics data analysis
data-analysis biostatistics statistics proteomics
8 months ago by Ariadna ▴ 20
0
votes
0
replies
538
views
News: Online course: Gene set enrichment analysis in R/Bioconductor
R Bioconductor GSEA GeneSetEnrichmentAnalysis
8 months ago by Physalia-courses ★ 2.6k
1
vote
3
replies
894
views
How to connect the tips of several phylogenetic trees with ggtree?
R tanglegram phylogenetic tree ggtree
8 months ago by Luca Arbore ▴ 10
1
vote
5
replies
1.1k
views
Extracting CDS Region of FFAR4 Gene Using Samtools from GRCh38 Reference Genome
samtools ccds grch38 genome cds
updated 8 months ago by ★ 1.3k • written 8 months ago by ▴ 40
1
vote
2
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911
views
How to extract and analyze variant sequences from gnomAD v4 exome VCF
samtools bcftools exome vcf genomics
8 months ago by Rohan ▴ 40
1
vote
3
replies
871
views
How to plot PCA for DEGs
DEG for PCA_plot
updated 8 months ago by ▴ 190 • written 8 months ago by ▴ 40
3
votes
6
replies
1.2k
views
Why only C > A,T,G and T > A,G,C mutations typically considered in 96 SBS context plots
Mutations SNV
8 months ago by BioStar22 • 0
2
votes
2
replies
724
views
help with finding start&and locations of gene list
gene locations
updated 8 months ago by 153k • written 8 months ago by ▴ 10
0
votes
5
replies
1.6k
views
Ensemble Service error
Ensembl Gene
updated 8 months ago by 153k • written 8 months ago by ▴ 140
0
votes
0
replies
433
views
Interpretation of WGCNA modules dendrogram
metadata sample WGCNA clustering dendrogram
8 months ago by tommasoasquini • 0
0
votes
0
replies
420
views
News: Introduction to Bayesian statistical modelling for biologists (online course)
Bayes biostatistics modelling course
8 months ago by Rosina Savisaar ▴ 10
0
votes
0
replies
424
views
Problems in Molecular Docking in Autodock vina
atom Boron autodock
8 months ago by Nibedita • 0
0
votes
2
replies
996
views
Problems with zero count values and mapping % in MaGeCK
CRISPR screen MaGeCK
8 months ago by DragosV • 0
2
votes
1
reply
637
views
ENRICHMENT USING CLUSTERPROFILER
clusterprofiler SOMASCAN proteins enrichment
updated 8 months ago by 89k • written 8 months ago by ▴ 20
3
votes
4
replies
971
views
CNV Analysis and Visualisation
visualization CNV analysis
updated 8 months ago by ▴ 80 • written 8 months ago by • 0
0
votes
0
replies
361
views
Viewing nexus de bruijn graphs
de-bruijn-graphs nexus
8 months ago by guntul ▴ 40
0
votes
3
replies
873
views
VEP Unable to process HGVS variants
python vep genome
updated 7 months ago by 45k • written 8 months ago by • 0
1
vote
2
replies
730
views
run snp2hla tool in windows subsytem for linux
snp2hla
updated 8 months ago by 45k • written 8 months ago by ▴ 140
5
votes
4
replies
1.8k
views
Best Practices for ATACseq for Performing Differential Accessibility Analysis
differential-accessibility csaw DESeq2 ATACseq
updated 3 months ago by ▴ 690 • written 8 months ago by ▴ 10
2
votes
1
reply
601
views
What's the point of integrating single cell data of different conditions?
integration transcriptomics Seurat single-cell
updated 8 months ago by ★ 19k • written 8 months ago by ▴ 10
0
votes
2
replies
588
views
mapping reads to consensus - O coverage regions
mapping consensus coverage
8 months ago by elina2410 • 0
2
votes
3
replies
1.0k
views
Write maf file (opposite of read.maf)
maf maftools r
7 months ago by Nona ▴ 90
121,908 results • Page 42 of 2439
Recent Votes
Tried building a compact sequence format with 4-bit storage
Comment: Tried building a compact sequence format with 4-bit storage
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
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Recent Replies
Comment: Tried building a compact sequence format with 4-bit storage by Pranava ▴ 10
I see, but the reason I was planning on using a 4bit system is so that there wouldn't be too much data loss but thank you for the suggesti…
Comment: Splice junctions plots for long-read seq data by alison.ludzki • 0
Thank you! I will check out miso!
Comment: Hifiasm is getting killed while trying to assemble a genome by pranavdatar01 • 0
I did subsample the data to 30x coverage. I did run hifiasm on it, the log file did show some contents, but hifiasm ended again, stating th…
Comment: Tried building a compact sequence format with 4-bit storage by Alex Reynolds 36k
Using four bits for storage won't beat 2bit, of course, but direct access to a sequence of interest sounds interesting and useful and might…
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…
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