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122,201 results • Page 609 of 2445
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2
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1.1k
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Python modules/code to generate triangulations of Solvent Excluded Surfaces
Proteins Visualization Python Molecular
4.3 years ago by Tzunami ▴ 10
0
votes
0
replies
820
views
Add SM group STAR
samtools variant RNA-seq calling GATK STAR
4.3 years ago by Lucy ▴ 170
3
votes
4
replies
1.3k
views
Sam file arrangement
BAM BED
updated 4.3 years ago by 90k • written 4.3 years ago by • 0
1
vote
1
reply
1.1k
views
Syntax error when running ScaleHD
repeats expansion illumina ScaleHD amplicon
updated 3.4 years ago by ▴ 60 • written 4.3 years ago by ▴ 210
2
votes
4
replies
2.8k
views
interpreting heatmap on metascape
metascape heatmap annotation
updated 2.8 years ago by 45k • written 4.3 years ago by • 0
0
votes
3
replies
1.4k
views
Methylome Data or DE Analysis
DE DESEQ2 Methylome
updated 4.3 years ago by 90k • written 4.3 years ago by ▴ 10
2
votes
13
replies
3.3k
views
gene expression of specifics gene
RNA-Seq
4.3 years ago by Bioinformatics1 ▴ 10
0
votes
6
replies
2.5k
views
how to create heat map using ggplot2 in R?
R
updated 4.3 years ago by 90k • written 4.3 years ago by • 0
2
votes
2
replies
1.3k
views
Can Exonerate return only the Cigar string?
Exonerate
updated 4.3 years ago by 45k • written 4.3 years ago by • 0
0
votes
3
replies
1.9k
views
What kinds of GSEA would be most appropriate for RNA-Seq Data?
rnaseq R
updated 4.3 years ago by 3.3k • written 4.3 years ago by ▴ 20
4
votes
6
replies
7.7k
views
Annotation Affymetrix probesets to Gene symbols
RNA-Seq R affymetrix gene
updated 4.3 years ago by ★ 90k • written 6.1 years ago by ▴ 130
3
votes
8
replies
5.9k
views
WGCNA adjust p value
statistics WGCNA
updated 15 months ago by • 0 • written 4.3 years ago by ▴ 10
0
votes
5
replies
2.1k
views
Removing specified range of bases from middle of the contigs and creating new sequences
Contigs Assembly fastafile
updated 4.3 years ago by 21k • written 4.3 years ago by ▴ 280
3
votes
2
replies
1.6k
views
Will this de novo transcriptome assembly be useful in looking at RNAseq differential expression?
de-novo-assembly
updated 2.2 years ago by 45k • written 4.3 years ago by ▴ 180
2
votes
3
replies
1.5k
views
Exonerate - using it in another project
Exonerate
updated 4.3 years ago by ★ 2.9k • written 4.3 years ago by • 0
0
votes
1
reply
910
views
How to caclulate polarity
python polarity AA
updated 4.3 years ago by 22k • written 4.3 years ago by • 0
0
votes
0
replies
1.1k
views
What is the difference between Protein-protein interactions (eg: PPI network from STRING database) network and protein functional interaction network…
interaction protein analysis ontology ReactomeFiviz database network protein-protein gene String
4.3 years ago by anandprem1792 ▴ 60
0
votes
3
replies
2.5k
views
How can I find matches between two csv files according to multiple columns using awk/bash?
awk genomics bash
updated 4.1 years ago by 5.9k • written 4.3 years ago by • 0
0
votes
0
replies
1.2k
views
configparser.NoOptionError: No option 'gene_regions' in section: 'mm10' : when use rgt-hint footprinting
ATAC-seq footprinting
4.3 years ago by 17318598206 ▴ 30
0
votes
0
replies
639
views
Is it possible to compare signals from separate BeadChips?
Illumina batch-effect BeadChips
updated 15 months ago by 45k • written 4.3 years ago by • 0
1
vote
3
replies
2.5k
views
No INFO/info value in headers
VCF Michigan-Imputation-Server
updated 4.3 years ago by 45k • written 4.3 years ago by • 0
1
vote
4
replies
2.6k
views
How do you add gene annotations from a Diamond Blastx tsv file to a csv file with RNAseq differential expression data?
BLASTx RNA-seq diamond
updated 2.2 years ago by 45k • written 4.3 years ago by ▴ 180
0
votes
0
replies
650
views
STAR aligner output report gives %2 uniquely aligned reads while
RNA-Seq HERV
4.3 years ago by mb86 • 0
0
votes
2
replies
2.2k
views
understanding snpEff/snpSift concordance output
snpEff snpSift SNP concordance
updated 4.3 years ago by • 0 • written 5.6 years ago by • 0
2
votes
1
reply
3.4k
views
results from SNPSift Concordance
SNPSift concordance snp
updated 4.3 years ago by • 0 • written 8.6 years ago by ▴ 390
0
votes
1
reply
1.1k
views
Job: Automation Engineer
Engineer
updated 4.3 years ago by 45k • written 4.3 years ago by ▴ 70
0
votes
6
replies
7.6k
views
featureCounts parameters for RNA-Seq
featurecounts RNA-Seq Subread ReadCounts
updated 4.3 years ago by • 0 • written 6.0 years ago by ▴ 50
0
votes
0
replies
764
views
RNAseq only paired ends reads using featurecounts, should I pay attention to count only reads match to one strand?
rna featurecounts paired
4.3 years ago by wang-yanfang • 0
0
votes
2
replies
1.4k
views
Best way to evaluate the relationship between protein and RNA abundance
RNA protein
4.3 years ago by haasroni • 0
0
votes
0
replies
734
views
is it possible to subset samples and reheader a vcf in a single step?
bcftools
4.3 years ago by curious ▴ 900
0
votes
2
replies
1.6k
views
How to obtain subpopulation specific allelic variants from a .vcf file using PLINK?
1000genomes vcf plink
updated 2.7 years ago by 45k • written 4.6 years ago by • 0
2
votes
3
replies
1.8k
views
Cuffmerge running time
Cuffmerge
updated 4.3 years ago by ★ 1.1k • written 4.3 years ago by ▴ 50
2
votes
5
replies
2.0k
views
Same strand, same QNAME different FLAG?
strand featureCounts SAM RNAseq
4.3 years ago by compuTE ▴ 140
0
votes
0
replies
1.1k
views
Cut-off value from qvalue package R for Manhattan plot
GWAS qvalue threshold significant plot manhattan rrBLUP
4.3 years ago by b.g.tamang ▴ 20
5
votes
8
replies
3.6k
views
Strand specific quantification with strand-splitted BAM files
featureCounts SAM strand RNAseq
updated 4.3 years ago by 103k • written 4.3 years ago by ▴ 140
0
votes
2
replies
1.1k
views
Combine haploid fastq's into diploid "individuals"
GATK pop-gen haplodiploid
4.3 years ago by timothy.delory ▴ 20
0
votes
0
replies
948
views
ABSOLUTE calls on CCLE cell-lines
Allele-specific LOH CNV ABSOLUTE CCLE
4.3 years ago by Nisha • 0
1
vote
2
replies
2.0k
views
How to download this genome?
genome
updated 4.3 years ago by 154k • written 4.3 years ago by ▴ 30
1
vote
2
replies
1.3k
views
Collect ITS sequences from bacterial genomes
rRNA ITS internal 16S transcribed taxonomy region
updated 4.3 years ago by ★ 30k • written 4.3 years ago by ▴ 50
0
votes
0
replies
654
views
Calculating frequencies for first-order Markov model given G+C content and CpG fraction
Markov model
4.3 years ago by valba • 0
4
votes
6
replies
2.0k
views
Differentially gene expression multispecies
Expression Multispecies Rnaseq differentially
updated 2.9 years ago by ▴ 40 • written 4.3 years ago by ▴ 40
2
votes
4
replies
7.4k
views
Going from Seurat object to DESeq2 analysis
DEG single-cell DESeq2 scRNAseq Seurat
updated 4.3 years ago by 4.2k • written 4.3 years ago by ▴ 50
2
votes
3
replies
1.5k
views
No out put from python function
Python
4.3 years ago by ThulasiS ▴ 90
4
votes
6
replies
3.2k
views
Measuring pairwise distances between residues/atoms in structural alignment of protein family
biopython protein alignment distance pairwise
updated 4.3 years ago by 22k • written 4.3 years ago by ▴ 70
0
votes
0
replies
895
views
VCFtools giving me a blank output for Tajima's D test at certain loci
Tajima population neutrality
4.3 years ago by milesandersonmn ▴ 20
0
votes
0
replies
649
views
Do you know a sofware to draw pedigrees + haplotypes?
mutation Haplotype pedigree Cyrilic sequencing
4.3 years ago by Negar • 0
1
vote
3
replies
5.5k
views
How to use 1000 Genomes data for LDheatmap package in R
SNP R lingkage ldheatmap heatmap
updated 4.3 years ago by ▴ 20 • written 10.0 years ago by ▴ 10
1
vote
4
replies
1.3k
views
aGPCR
GPCR
4.3 years ago by keyajoshi1996 • 0
0
votes
0
replies
551
views
Secondary structure information using cpptraj
CPPTRAJ
4.3 years ago by keyajoshi1996 • 0
3
votes
6
replies
2.9k
views
BWA MEM fail to open file for output SAM
sam index bwa output
updated 4.3 years ago by 90k • written 4.3 years ago by ▴ 60
122,201 results • Page 609 of 2445
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 GenoMax 154k
Each database has their own method of annotation/validation. Depending on resources available there may be a lag between the databases in t…
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Wu-Sheng Zhang • 0
Hi @arup , thank you very much for your suggestions, and here are the results -- they seems correct. May I have your suggestions? Thank you…
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding by samuel.a.odonnell ▴ 640
I don't believe merqury ignores softmasked (lower case) nucleotides so I don't think that is the case. From what it sounds like, during th…
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)?
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