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122,200 results • Page 653 of 2444
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1
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14
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6.7k
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RNAseq: What is the difference between the units log2 (tpm + 0.001) and log2 (norm_count + 1)
IsoPct units RNAseq
4.5 years ago by muet-10 • 0
1
vote
6
replies
2.8k
views
pheatmap input file
r Qiime2 pheatmap
4.5 years ago by Bioinfonext ▴ 480
1
vote
1
reply
3.3k
views
k-mer distribution to estimate the heterozygosity of my assembly
kmer Assembly pacbio purge_dups
updated 4.5 years ago by ▴ 230 • written 5.0 years ago by ▴ 350
0
votes
0
replies
777
views
JUM output Splicing events Visualization tools
LeafViz Leafcutter JUM
4.5 years ago by Shashi Kanth ▴ 10
4
votes
4
replies
3.8k
views
How to interpret ScanPy scatter plots for QC filtering?
Python jupyter-lab ScanPy RNA-Seq scRNA-seq
4.5 years ago by Pratik ★ 1.1k
1
vote
5
replies
1.8k
views
Variant discordant alignment HISAT2
alignment HISAT2 RNA-seq assembly Galaxy
updated 4.5 years ago by • 0 • written 4.5 years ago by • 0
1
vote
2
replies
1.9k
views
Only output SNPs in bcftools
bcftools SNPs
4.5 years ago by NewtoBioinfo • 0
0
votes
3
replies
1.8k
views
Make map file with recombination rate using plink?
germline plink
updated 4.5 years ago by 2.9k • written 4.5 years ago by ▴ 900
1
vote
2
replies
1.8k
views
STAR aligner fatal error
mapping STAR nanopore
updated 4.5 years ago by ▴ 70 • written 4.5 years ago by • 0
0
votes
6
replies
68k
views
Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent
R heatmap error
updated 4.5 years ago by • 0 • written 6.7 years ago by ▴ 50
0
votes
1
reply
1.4k
views
Job: Bioinformatician
genetics python java php
updated 4.4 years ago by 45k • written 4.5 years ago by • 0
0
votes
4
replies
1.7k
views
how to plot one-dimeson heatmap using R
R heatmap
updated 4.5 years ago by 36k • written 4.5 years ago by ▴ 10
10
votes
6
replies
5.9k
views
6 follow
Is there a tool to draw local ancestry plots per chromosome?
ideogram ancestry lamp-ld
updated 3.3 years ago by 45k • written 10.0 years ago by ▴ 90
5
votes
7
replies
2.0k
views
Creating numbered gene sets from a list of genes
Bash awk geneset
updated 4.5 years ago by 21k • written 4.5 years ago by ▴ 30
0
votes
1
reply
936
views
Counting column values before Fisher's test ends with NULL in R
statistics NGS R
updated 4.5 years ago by 12k • written 4.5 years ago by ▴ 30
4
votes
6
replies
2.8k
views
Cons of Smith-Waterman Alignment
Smith-Waterman Genomics Alignment DNA Sequences
updated 4.5 years ago by ★ 3.0k • written 4.5 years ago by ▴ 30
0
votes
0
replies
874
views
Tajima'S D for targeted sequencing data
DnaSP SNPs SnpPanel angsd TajimaD
4.5 years ago by meg.nat86 • 0
1
vote
0
replies
1.1k
views
Can you generate a mappability mask with STAR (or another splice-aware aligner)?
STAR mappability SNPable bwa
4.5 years ago by mercerf93 ▴ 10
0
votes
0
replies
891
views
Focused pathway analysis
fgsea clusterProfiler GSEA KEGG pathway
4.5 years ago by cwwong13 ▴ 40
0
votes
8
replies
1.7k
views
Assembly copy from subdirectory
Assembly
updated 4.5 years ago by 21k • written 4.5 years ago by • 0
8
votes
6
replies
5.7k
views
How tximport work with gencode transcripts?
RNA-Seq R
updated 4.3 years ago by ★ 90k • written 7.4 years ago by ▴ 610
0
votes
2
replies
3.2k
views
Generating a background file to be used by Homer for motif identification
homer
4.5 years ago by gkunz ▴ 30
9
votes
5
replies
2.9k
views
How to plot "Distribution of SNPs per Mbp"
plot
updated 4.5 years ago by 36k • written 4.5 years ago by ▴ 40
5
votes
9
replies
2.4k
views
For loop for MUMmer
shell bash forloop
updated 4.5 years ago by 21k • written 4.5 years ago by ▴ 80
2
votes
2
replies
1.4k
views
Problem setting blastdb in linux
blastdb blastall
updated 4.5 years ago by ★ 30k • written 4.5 years ago by ▴ 280
0
votes
0
replies
818
views
Ccle miRna data units
Ccle Mirna-seq
4.5 years ago by Nihanth • 0
2
votes
4
replies
1.6k
views
Batch Effect
r RNA-seq
updated 4.5 years ago by ▴ 250 • written 4.5 years ago by ▴ 130
0
votes
1
reply
1.6k
views
How to plot LD decay per chromosome
LDdecayplot LDdecay
updated 4.5 years ago by ★ 4.0k • written 4.5 years ago by ▴ 40
2
votes
1
reply
986
views
Can anyone please tell me whether I should go for multivariable analysis with my data in this condition?
statistics multivariate
updated 4.5 years ago by ▴ 160 • written 4.5 years ago by ▴ 40
1
vote
2
replies
1.1k
views
RNA-seq Normalisation methods to compare using raw miRNA data
miRNA RNA-seq normalisation
4.5 years ago by raavi21198 ▴ 20
0
votes
4
replies
2.4k
views
struct.error in MACS2 callpeak
ChIP-seq MACS2
4.5 years ago by ty0017 • 0
0
votes
0
replies
1.2k
views
HaplotypeCaller run time ?
WGS Haplotypecaller GATK
4.5 years ago by quentin54520 ▴ 120
2
votes
4
replies
1.8k
views
Close homologs search
search BLAST homologs
updated 4.5 years ago by ★ 30k • written 4.5 years ago by ▴ 50
0
votes
4
replies
4.6k
views
High Sierra vs Catalina vs Big Sur
MAC OS
4.4 years ago by ddraki2008 • 0
0
votes
0
replies
1.1k
views
Misunderstanding on calculating Ka/Ks values
Nucleotide
4.5 years ago by Abdukhalim Khon • 0
6
votes
13
replies
9.1k
views
Choosing a high soft thresholding power in WGCNA, is it reasonable?
WGCNA
updated 4.4 years ago by 3.9k • written 4.6 years ago by ▴ 10
0
votes
0
replies
753
views
Where to find hepatitis virus infectious status information available in TCGA or ICGC database when study HCC?
manipulation HCV clincal data HCC ICGC
3.2 years ago by Dude • 0
1
vote
8
replies
5.4k
views
6 follow
DESeq2 count matrix read in
deseq2 R
updated 2.7 years ago by 45k • written 4.5 years ago by ▴ 550
0
votes
0
replies
634
views
Need help contig assembly
Contig
updated 4.5 years ago by 45k • written 4.5 years ago by • 0
2
votes
3
replies
1.6k
views
MACS2 does not giving same result before and after chromosome extraction from bam file
chromosome samtools extract peakcalling macs2
updated 4.5 years ago by 11k • written 4.5 years ago by ▴ 130
0
votes
0
replies
1.5k
views
findMotifs vs findMotifsGenome, inequality of results
homer motifs
4.5 years ago by boczniak767 ▴ 880
10
votes
13
replies
9.4k
views
snp density plot
snp
updated 4.5 years ago by ▴ 40 • written 6.1 years ago by ▴ 230
9
votes
11
replies
6.3k
views
BED file: Find intervals that overlap a certain percentage and keep the longest one
Bed bedtools bash bedops
4.5 years ago by biomonte ▴ 220
1
vote
0
replies
1.1k
views
Job: Senior Bioinformatician in Molecular Screening and Omics Research - AstraZeneca, Cambridge, UK
omics screening AstraZeneca
updated 4.4 years ago by 45k • written 4.5 years ago by ▴ 230
0
votes
2
replies
1.7k
views
What is current the best available rat lung single cell RNA seq dataset for cell type annotation? any recommendations ?
SingleR scRNAseq
4.5 years ago by FantasticAI ▴ 60
0
votes
1
reply
2.8k
views
IGV not showing transcripts
transcripts IGV
updated 4.5 years ago by 90k • written 4.5 years ago by ▴ 20
0
votes
0
replies
864
views
How can I convert a molecule written in SMILE in SMART?
superimposition ligands open_babel
4.5 years ago by Agnese • 0
1
vote
1
reply
1.4k
views
Homer motif analysis
Homer R motif
updated 4.5 years ago by 11k • written 4.5 years ago by • 0
0
votes
4
replies
3.7k
views
KaKs calculator
Nucleotide Substitutions
updated 4.3 years ago by • 0 • written 4.5 years ago by • 0
1
vote
0
replies
988
views
How does FDRtool work?
rnaseq fdrtool deseq2 r pvalue
4.5 years ago by emmagervide ▴ 10
122,200 results • Page 653 of 2444
Recent Votes
Can EdgeR of DeSeq be used for Single-cell RNA-seq?
Answer: Getting the overlap between two GTF files
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria
Converting GFF to GTF
Answer: best practice for diploid variant calling
Answer: Can i use orthofinder for small protein datasets and not full proteome?
Comment: Can i use orthofinder for small protein datasets and not full proteome?
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Recent Replies
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by thomas.heigl.ibk ▴ 10
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 ▴ 10
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(…
Answer: Finding Sentrix ID in HM450K arrays by yura.grabovska ▴ 890
``` ##Using R, illuminaio from Bioconductor library(illuminaio) temp.idat <- readIDAT(file = "200379120087_R02C02_Grn.idat") tem…
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