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122,202 results • Page 672 of 2445
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2
votes
2
replies
1.5k
views
Trouble with plotMA
plotMA DeSeq2 R
updated 3.9 years ago by 90k • written 4.6 years ago by • 0
4
votes
3
replies
2.5k
views
Normalize by contig size BEFORE RPKM normalization?
virus normalization metagenomics edgeR RPKM
updated 4.6 years ago by ★ 3.3k • written 4.6 years ago by ▴ 160
0
votes
0
replies
667
views
How does changes in pH change the conformation of a protein - Software
quaternary pH structure protein
4.6 years ago by roybatty269 • 0
1
vote
4
replies
1.1k
views
Error in chopping alignment files for each chromosome
alignment
updated 4.6 years ago by 154k • written 4.6 years ago by • 0
1
vote
5
replies
1.7k
views
Could someone help me check what genomic position is this variant nomenclature referring to ?
nomeclature
updated 4.6 years ago by 21k • written 4.6 years ago by ▴ 900
1
vote
0
replies
930
views
Calculating Fst from low coverage data using genotype likelihoods
vcftools fst population_differentiation
4.6 years ago by Jautis ▴ 580
0
votes
3
replies
2.7k
views
customized gene not show in the output from cellranger count even if I have added to the reference genome database
gene scRNA cellranger
updated 4.6 years ago by ▴ 40 • written 4.6 years ago by ▴ 150
0
votes
0
replies
686
views
Creating phylogenetic trees for a full genome at once?
genomic Phylogeny
4.6 years ago by blur ▴ 280
1
vote
2
replies
1.3k
views
fastq-dump for downloading multiple sets reads?
illumina ncbi fastq-dump genomes
4.6 years ago by c.e.chong ▴ 60
2
votes
11
replies
3.1k
views
Using snakemake in order to download reads and run hisat2 mapping
hisat2 snakemake python
updated 4.6 years ago by 23k • written 4.6 years ago by ▴ 140
0
votes
1
reply
821
views
Clinical Data Analysis in R for significant difference between 2 groups in R
testing Biostatistics Significant R
updated 4.6 years ago by ★ 90k • written 4.6 years ago by • 0
0
votes
1
reply
1.0k
views
Distance Correlation Matrix Intrepretation
statistics correlation R
updated 4.6 years ago by ★ 90k • written 4.6 years ago by • 0
2
votes
6
replies
2.9k
views
How can I draw this plot?
bcftools roh-calling roh samtools
updated 3.8 years ago by ▴ 350 • written 4.6 years ago by ▴ 260
2
votes
2
replies
1.4k
views
How to associate secondary structure to protein sequence
secondary python structure pdb database
4.6 years ago by francesco.costa.11 ▴ 30
1
vote
3
replies
1.0k
views
How to find variants which are not present in second file
vcf
updated 4.6 years ago by 166k • written 4.6 years ago by ▴ 40
0
votes
2
replies
1.9k
views
HaplotypeCaller output mode
GATK HaplotypeCaller
4.6 years ago by puddingmeow516 ▴ 10
1
vote
3
replies
1.4k
views
Where to find 'nr. Non-redundant GenBank...' the peptide sequence database?
database genbank
updated 4.6 years ago by 154k • written 4.6 years ago by ▴ 20
4
votes
5
replies
4.4k
views
Varying read length distribution after running Trimmomatic
RNAseq pairedend Trimmomatic
updated 4.6 years ago by 154k • written 4.6 years ago by ▴ 140
1
vote
0
replies
847
views
News: Online Training -low-coverage Whole Genome Sequencing
Genome SNPs NGS WholeGenomeSequencing
4.6 years ago by Physalia-courses ★ 2.7k
0
votes
0
replies
774
views
News: Online Training -Generalised Linear Models in R
GLMs statistics GeneralisedLinearModels R
4.6 years ago by Physalia-courses ★ 2.7k
0
votes
5
replies
1.6k
views
conversion from genomic to gene coordinates in a large file
plink
4.6 years ago by storm1907 ▴ 30
2
votes
1
reply
2.0k
views
CUDA_ERROR_COMPAT_NOT_SUPPORTED_ON_DEVICE when running guppy basecaller
basecalling ont guppy nanopore cuda
4.6 years ago by eoneill627 ▴ 20
1
vote
3
replies
1.5k
views
Assigning small RNA reads
featureCount smallRNA rna rna-seq sequencing
updated 4.6 years ago by 9.0k • written 4.6 years ago by ▴ 10
2
votes
1
reply
2.0k
views
CNVkit result interpretation
CNVkit result cns
updated 2.3 years ago by ▴ 640 • written 4.6 years ago by ▴ 40
0
votes
1
reply
1.2k
views
Using RPKM to compare gene expression between samples
rnaseq normalization rpkm
updated 4.6 years ago by ★ 7.8k • written 4.6 years ago by • 0
1
vote
6
replies
1.7k
views
Grepping samples out of vcf and writing them to a new file
VCF grep bgzip bcftools
4.6 years ago by Kath__ ▴ 10
2
votes
6
replies
23k
views
How to explain the MA plot for differential expression analysis in RNA-seq data?
rna-sequencing graphs analysis
4.6 years ago by ashwing.kofficial ▴ 10
2
votes
1
reply
1.3k
views
Phenotype Enrichment Analysis vs Gene Enrichment Analysis
enrichment gene phenotype
updated 4.6 years ago by 56k • written 4.6 years ago by ★ 9.6k
0
votes
0
replies
490
views
Where can I find the ggKbase wrapper scripts?
ggKbase 16s.sh
4.6 years ago by Rui ▴ 50
0
votes
6
replies
3.8k
views
Microarray data analysis in R
agilent single-colour microarray
4.3 years ago by smrutimayipanda ▴ 20
0
votes
0
replies
992
views
Forum: CADD Error in EXOMISER
exomiser cadd
4.6 years ago by shwetan • 0
0
votes
1
reply
1.1k
views
Gene locations do not match
ChIP-Seq
updated 4.6 years ago by 90k • written 4.9 years ago by • 0
0
votes
3
replies
1.9k
views
Synonymous and asynonymous sites in Ka/Ks
Ka Ks
updated 4.6 years ago by 103k • written 4.6 years ago by ▴ 60
0
votes
1
reply
2.2k
views
ChIPSeeker Help for Annotating Peaks
ChIP-Seq atac-seq software error
updated 4.6 years ago by ▴ 220 • written 5.0 years ago by • 0
9
votes
4
replies
8.6k
views
How to filter out a list of specific genes from the DESeq object in R - bulk RNA-seq differential expression
R bulk object DESeq2 filter
4.6 years ago by msimmer92 ▴ 310
5
votes
7
replies
3.8k
views
EBI API GWAS query over gene
GWAS API EBI Python
updated 4.5 years ago by ▴ 30 • written 4.6 years ago by ▴ 170
4
votes
7
replies
3.5k
views
How to choose one TSS for a gene
transcription site tss start
4.6 years ago by GG • 0
3
votes
5
replies
2.7k
views
Mapping RNA seq reads from bed file to genes
RNAseq gene-expression tpm
4.6 years ago by jrose ▴ 30
0
votes
2
replies
970
views
Both mate pairs aligning to same contig counts
paired_reads samtools_coverage
4.6 years ago by Matan • 0
0
votes
0
replies
986
views
News: Call for abstracts BioSB 2021!
biosb conference dutch
updated 4.4 years ago by 45k • written 4.6 years ago by ▴ 230
1
vote
2
replies
3.2k
views
help to download Repbase repeatmasker
next-gen assembly software error
updated 4.6 years ago by ▴ 10 • written 5.2 years ago by • 0
0
votes
2
replies
1.9k
views
Why do paired ends map to same coordinates of a scaffold?
reads map magicblast SRA
4.6 years ago by wmorgan ▴ 20
0
votes
1
reply
777
views
Yeast genome annotation: How to predict genes and CDS of them?
ncbi yeast annotation
updated 2.7 years ago by 45k • written 4.6 years ago by • 0
0
votes
0
replies
574
views
inquiry related to docking
docking
4.6 years ago by rheab1230 ▴ 150
0
votes
3
replies
3.0k
views
demultiplex paired end fastq file with mixed samples with barcode
RNAseq fastq demultiplex
updated 4.6 years ago by 154k • written 4.6 years ago by ▴ 40
4
votes
4
replies
4.2k
views
1000G Tabix download: EOF marker is absent
1000Genomes Tabix vcf-subset bgzip
updated 4.6 years ago by 2.9k • written 4.6 years ago by ▴ 40
0
votes
0
replies
2.0k
views
how to get feature importance after SVM
high_dimensional SVM R
4.6 years ago by pt.taklifi ▴ 70
9
votes
9
replies
3.4k
views
RNA-seq de novo assembly alignment quality assessment
trinity rnaseq denovo assembly
4.6 years ago by sarahmanderni ▴ 130
0
votes
0
replies
1.1k
views
Preparation of a matrix of expression values of RNA-seq for input data of ssGSEA
ssGSEA RNA-seq
4.6 years ago by Apprentice ▴ 190
0
votes
1
reply
4.2k
views
Is there a way to remove certain chromosomes from a GRanges Object?
GenomicRanges Package GRanges
updated 4.6 years ago by 21k • written 4.6 years ago by ▴ 110
122,202 results • Page 672 of 2445
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strong appearing variant not found by haplotypecaller in -ERC mode and deepvariant but with haplotypecaller in normal mode
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Recent Replies
Comment: Visualize methylation status in Pacbio Hifi read by cmdcolin ★ 4.4k
(as the JBrowse dev) I'm glad to hear this. if you see any trouble with it feel free to let me know, I have tried to keep up to date with m…
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Wu-Sheng Zhang • 0
Got it! I will try to switch their name and re-run the cellranger arc. Thank you very much, @arup !
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Arup Ghosh 3.5k
The barcode files with 24nt read length W71_LUNGrep2_S6_L001_R3_001.fastq.gz and W71_LUNGrep2_S6_L002_R3_001.fastq.gz should be the R2.
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!
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