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122,200 results • Page 615 of 2444
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3
votes
1
reply
1.3k
views
Bioconductor package specific website
Bioconductor Rstats R
updated 4.4 years ago by ★ 1.2k • written 4.4 years ago by ★ 2.0k
0
votes
0
replies
764
views
Indel frequency analysis from CRISPR modification using sequencing data.
CRISPR Indel Cas9 frequency site cut
4.4 years ago by ms3389 • 0
0
votes
0
replies
918
views
Nebula .cram to .bam via samtools
bam analysis cram samtools
4.4 years ago by christian.palmer • 0
18
votes
3
replies
11k
views
Is There Any Freeware To Analyze Electrophoresis Gels?
analysis software
updated 4.4 years ago by ▴ 10 • written 15.6 years ago by ▴ 150
0
votes
0
replies
951
views
Strelka2 stomatic calls, where is the GT tag ?
strelka annovar variant
4.4 years ago by simplitia ▴ 130
8
votes
2
replies
3.5k
views
How to run vg giraffe for sv genotyping?
vg
updated 4.4 years ago by ▴ 800 • written 4.4 years ago by 24k
0
votes
1
reply
1.1k
views
Identifying novel proteins from bacterial genomes
annotations database bacteria
updated 4.4 years ago by ▴ 590 • written 4.4 years ago by • 0
0
votes
1
reply
1.2k
views
converting genomic version for annovar database?
annovar variant
updated 4.4 years ago by ▴ 580 • written 4.4 years ago by ▴ 130
0
votes
2
replies
4.6k
views
how to merge a subset dataset back to master seurat object
scRNA RNAseq
updated 4.4 years ago by ★ 19k • written 4.4 years ago by ▴ 250
0
votes
0
replies
648
views
Comparative methylation between two isogenic strains of E coli
nanopolish isogenic methylation
4.4 years ago by lkthomp06 • 0
2
votes
5
replies
1.8k
views
How to automatically distinguish single vs. bulk GEO datasets (in ARCHS4 collection or in general) ?
scRNAseq
4.3 years ago by Alexander ▴ 220
0
votes
1
reply
1.1k
views
Parallelize microRNA targets
RNA-Seq
updated 4.3 years ago by 45k • written 4.4 years ago by • 0
2
votes
2
replies
5.3k
views
Recommended PC Hardware for Molecular Dynamics in 2021
PC configuration hardware moleculardynamics
updated 4.4 years ago by ★ 30k • written 4.4 years ago by • 0
4
votes
3
replies
1.5k
views
FeatureCounts dont read all features
featureCounts
updated 4.4 years ago by 154k • written 4.4 years ago by • 0
2
votes
1
reply
957
views
Validate TCGA DEGs with GEOdatabase
DEGs TCGA GEOdatabase
updated 4.4 years ago by 3.3k • written 4.4 years ago by • 0
0
votes
2
replies
1.3k
views
What are the conventions/how to tell what a GSM has had done to it?
GSE GSM methylation minfi GEOquery
updated 4.4 years ago by ▴ 30 • written 4.5 years ago by • 0
1
vote
1
reply
1.4k
views
How can the output be renamed when converting genbank files into GFF3 format with BioPerl?
gff3 bioperl rna-seq genbank genbank2gff3.pl
4.4 years ago by Constanza • 0
3
votes
6
replies
2.0k
views
Strand specific library
htseq
updated 4.4 years ago by 4.2k • written 4.4 years ago by ▴ 30
9
votes
4
replies
6.6k
views
Can I perform scRNAseq data integration without loosing features?
scRNAseq anchor integration Seurat features
4.4 years ago by joker33 ▴ 150
0
votes
0
replies
2.0k
views
How to create an upset plot with a count of genes per pathway in cluster-profiler?
enrichment R dose plot gene upset
4.4 years ago by DN99 ▴ 20
2
votes
2
replies
2.0k
views
DESeq2 results difference using contrast and single conditions
DESeq2 RNAseq
4.4 years ago by User000 ▴ 750
4
votes
6
replies
4.3k
views
interaction energy using foldx to calculate stability
chains foldx protein stability
4.3 years ago by sba5k • 0
0
votes
0
replies
1.1k
views
Multiple tests between multiple conditions and covariates with sleuth
kallisto R sleuth
4.4 years ago by danjs116 • 0
0
votes
6
replies
2.3k
views
Can it be useful to depict variable genes using non-log transformed counts?
variance rnaseq heatmap
updated 4.2 years ago by 90k • written 4.4 years ago by ▴ 160
2
votes
5
replies
1.8k
views
opening downloaded files from STRING protein network without R
protein STRING network
updated 2.7 years ago by 45k • written 4.4 years ago by • 0
0
votes
4
replies
1.8k
views
Quantify transcriptomic shift between two conditions for each cluster
scRNAseq seurat singlecell RNAseq
3.3 years ago by Wocher33 ▴ 10
3
votes
5
replies
1.8k
views
False positive adaptor findings on FastQC/MultiQC using BBMaps randomreads.sh
FastQC adaptors BBMap simulated reads
updated 4.4 years ago by 154k • written 4.4 years ago by ▴ 20
1
vote
3
replies
1.9k
views
Guided bioinformatics Python projects
python learning
updated 4.3 years ago by 45k • written 4.4 years ago by • 0
0
votes
0
replies
759
views
SKAT burden analysis in R
association analysis variant skat rare
4.4 years ago by afergused • 0
0
votes
0
replies
710
views
Annotating variants from a sequence and list of position-specific variants
variant-effect-predictor variant-annotation vep
4.4 years ago by manaswwm ▴ 570
1
vote
3
replies
1.2k
views
Finding homologs in BLASTN
genomics comparative
updated 4.4 years ago by 154k • written 4.4 years ago by • 0
1
vote
2
replies
1.3k
views
Mapsplice2
Mapsplice2
updated 4.3 years ago by 45k • written 4.4 years ago by • 0
1
vote
4
replies
4.1k
views
RNAseq - GBFF cannot be converted to GTF
Genome GBFF GTF NCBI RNAseq
4.4 years ago by sacdefruits • 0
0
votes
0
replies
880
views
Caffeinate alternative for Docker
Docker Caffeinate
updated 3.0 years ago by 45k • written 4.4 years ago by • 0
2
votes
1
reply
1.4k
views
command line VEP and VEP web interface return different results.
ensembl vep
updated 4.4 years ago by 24k • written 4.4 years ago by ▴ 420
0
votes
2
replies
1.3k
views
how to produce plot below using R
RNA-Seq plot circus
4.4 years ago by adR ▴ 130
2
votes
1
reply
1.2k
views
DNA Methylome and RNA-seq intersect
RNA-seq Methylome DNA
updated 4.4 years ago by ▴ 50 • written 4.4 years ago by ▴ 370
0
votes
4
replies
1.6k
views
Can Omni-C reads be used for genome polishing?
Omni-C polish genome
4.4 years ago by Biostar • 0
1
vote
9
replies
3.5k
views
bioMart biotype assignment
biomart
4.3 years ago by imaparna27 ▴ 20
1
vote
6
replies
3.2k
views
How to Add FORMAT column from VCF file to table?
snp vcftools vcf vep
updated 2.1 years ago by • 0 • written 4.4 years ago by ▴ 20
0
votes
5
replies
2.0k
views
BGZF file looks weird
BGZF
4.3 years ago by HL ▴ 10
4
votes
1
reply
1.3k
views
IGV sequence name error .sam file
sam graphmap IGV
updated 4.4 years ago by ★ 5.2k • written 4.4 years ago by ▴ 180
0
votes
0
replies
603
views
lncrna positive control gtex
gtex lncrna
updated 4.4 years ago by 90k • written 4.4 years ago by • 0
0
votes
0
replies
903
views
Need help interpreting CoGe SynMap result
genome genomics
updated 2.7 years ago by 45k • written 4.4 years ago by ▴ 80
0
votes
0
replies
744
views
FISH Probe bed file
Vysis Cytogenetics FISH
4.4 years ago by Jng • 0
5
votes
4
replies
2.0k
views
Convert missing genotype ./. to homozygous 0/0 in vcf
vcf
updated 4.4 years ago by ▴ 480 • written 4.4 years ago by ▴ 750
0
votes
6
replies
2.4k
views
How to convert gene names to GO term?
databse
4.3 years ago by dpc ▴ 250
0
votes
1
reply
2.0k
views
bamdst gives error "EOF marker is absent. The input is probably truncated."
bwa samtools bamdst
updated 4.2 years ago by ▴ 390 • written 4.4 years ago by ▴ 70
0
votes
0
replies
699
views
Starting GWAS with Plink
GWAS
4.4 years ago by dec986 ▴ 380
0
votes
0
replies
680
views
How to find the genes within MetaCyc pathways?
database
4.4 years ago by dpc ▴ 250
122,200 results • Page 615 of 2444
Recent Votes
strong appearing variant not found by haplotypecaller in -ERC mode and deepvariant but with haplotypecaller in normal mode
Answer: How can I easily remove overlapping transcripts, keeping only longest transcript
Answer: Log2 transformation is well used, but is there a good paper that can be used as
Answer: Flatten a GTF
Answer: RNA-seq - Creating SAF from NCBI gff for Subread featureCounts - keep 'gene' or
Can EdgeR of DeSeq be used for Single-cell RNA-seq?
Answer: Getting the overlap between two GTF files
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Recent Replies
Comment: ID unifiying across different datasets by zizigolu ★ 4.4k
Thanks a lot to be helpful I’m trying to build a complete `UniProtID` to `GeneSymbol` lookup table and I’m running into a wall. I’ve alrea…
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by thomas.heigl.ibk ▴ 20
thanks for the quick reply. i posted the screenshot. gatk-internally, there is still the difference using -ERC or not, priot is getting …
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by thomas.heigl.ibk ▴ 20
here the igv view. showing the histogram for all samples plus the reads for one: ![enter image description here][1] and expanded view of …
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Arup Ghosh 3.5k
Check the read lengths to make sure the files are correct.
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by Pierre Lindenbaum 166k
> Any suggestions or help you could share please, show us an IGV screenshot of the position GATK realign the reads locally, discards read…
Comment: Can i use orthofinder for small protein datasets and not full proteome? by alexandrakortsi • 0
By sequence. Thank you for your response!
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding by xinguok794 ▴ 10
Thank you for your reply! Unfortunately, despite running YAHS with `--no-contig-ec`, the QV value of the resulting FASTA file did not impro…
Comment: Subsetting before QC in Spatial Transcriptomics by Kent ▴ 30
Hi Kevin, Thanks for the detailed explanation. Due to the characteristics of the datasets, we initially used very lenient quality control…
Comment: Midpoint rooting IQTREE newick file moves node support around by Luca Arbore ▴ 10
Thank you very much Kevin, it worked!
Comment: ID unifiying across different datasets by GenoMax 154k
In this case the entry notes that this is likely the product of a pseudogene: https://www.uniprot.org/uniprotkb/Q5VTE0/entry and existence …
Comment: Comparison of different RNAseq data sets by DrSmad ▴ 10
Each lab contributes both control and LPS. Example, for cell line A_lab1 did and analysis on control and LPS-6h. Cell line B_lab2 did contr…
Comment: ID unifiying across different datasets by zizigolu ★ 4.4k
sorry, why some gene names are often lacking though the Uniprot ID is still valid (using biomart)?
Comment: snpEff: Unsupported structural variant types by shpak.max ▴ 70
Unfortunately, while it ran without a problem initially, when I checked the run screen today, I saw the following error message (and unlike…
Comment: ID unifiying across different datasets by GenoMax 154k
You can use the [**ID mapping tool**][1] from UniProt site (third ID did not map from the list above): From To P68104 ENSG0000015…
Answer: The geo samples is not having sentrix id and sentrix position. But this informat by yura.grabovska ▴ 890
Crosspost from related question: https://www.biostars.org/p/9616466/#9616534 ``` ##Using R, illuminaio from Bioconductor library(…
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