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122,200 results • Page 661 of 2444
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What determine if a panel can be used for copy number analysis?
panel copy number targeted
updated 4.5 years ago by ★ 3.0k • written 4.5 years ago by ▴ 60
2
votes
3
replies
2.0k
views
Need suggestions to combine the missense variants pathogenicity prediction scores generated by SIFT, CADD, REVEL, PolyPhen, MPC, etc. to prioritize/s…
Missense PredictionTools
updated 4.4 years ago by 45k • written 4.5 years ago by ▴ 10
1
vote
3
replies
2.5k
views
How to make a vcf file using GWAS Catalog all_association.tsv file
GWAS VCF genetic association CATALOG
updated 4.5 years ago by 166k • written 4.5 years ago by ▴ 30
2
votes
2
replies
2.0k
views
gffread doesn't convert gff to gtf (blank file)
gffread bash
updated 4.5 years ago by 9.3k • written 4.5 years ago by ▴ 10
0
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1
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1.2k
views
How to download dataset with paired 16S and shotgun from HMP?
16S HMP shotgun
4.5 years ago by mail2steff ▴ 70
4
votes
10
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7.8k
views
how to use the samtools filtering expression ?
samtools
updated 2.7 years ago by 45k • written 4.5 years ago by • 0
0
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0
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648
views
Assemble 3'mRNAseq with standard RNAseq
stringtie RNAseq assembly 3mRNAseq
4.5 years ago by Shred ★ 1.6k
1
vote
0
replies
1.0k
views
News: Comprehensive benchmarking of software for mapping whole genome bisulfite data
Methylation NGS Epigenetics Bisulfite
4.5 years ago by David Langenberger 11k
0
votes
2
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1.6k
views
Find all genes in multiple regions
ucsc ensembl biomart
updated 4.5 years ago by 14k • written 4.5 years ago by • 0
2
votes
4
replies
1.9k
views
How to capture the position of SNPs from the gene's locations
Bedtools Genome SNPs
4.5 years ago by Kumar ▴ 170
0
votes
0
replies
633
views
Many OTUs on chart
bracken Megan biom kraken
updated 4.5 years ago by 90k • written 4.5 years ago by • 0
1
vote
1
reply
868
views
Can I Illumina sequence with a polymerase that leaves -da overgangs?
sequencing illumina
updated 4.5 years ago by 90k • written 4.5 years ago by ▴ 40
3
votes
6
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5.3k
views
Bamtools stats and samtools flagstat produce different results and confusing my sambamba output.
sambamba bamtools samtools
4.5 years ago by DNAngel ▴ 260
1
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1
reply
1.4k
views
Pathway network
Reactome Pathway cytoscape KEGG igraph
updated 4.5 years ago by 27k • written 4.5 years ago by ▴ 550
0
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0
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898
views
porthomcl - executing only the certain step of procedures
threading porthomcl orthomcl thread
4.5 years ago by seok1213neo ▴ 40
0
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1
reply
1.1k
views
Error in using USEARCH - Bad line 5 in FASTQ file 'sample_R1.fastq': expected '@'
input usearch fastq fastqfile
updated 4.5 years ago by ★ 30k • written 4.5 years ago by • 0
3
votes
1
reply
1.9k
views
how to define open-pangenome?
python fasta genome dna clustering
updated 4.5 years ago by ▴ 30 • written 4.7 years ago by ▴ 120
1
vote
3
replies
1.3k
views
edgeR batch correction
edger batch
4.5 years ago by barix ▴ 20
0
votes
0
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707
views
Code for simulation of data sets
simulation
updated 4.5 years ago by 45k • written 4.5 years ago by • 0
0
votes
1
reply
1.9k
views
Extracting Read and mates having variant positions Using BAM file vcf file in Python using pysam/ bamnostics
NGS_DATA PYSAM Python BAM_FILE
updated 4.4 years ago by 45k • written 4.5 years ago by • 0
0
votes
0
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1.0k
views
Fatal error: exit code 1 () using make.shared
galaxy metadata metagenomics mothur error
4.5 years ago by elfellah.aymane00 • 0
1
vote
2
replies
1.3k
views
how to identify if a contig.fa file comes from IDBA or Spades?
assembler
4.5 years ago by leranwangcs ▴ 150
0
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9
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3.0k
views
How get density plot TSS region for genes of interest
Chipseq
updated 15 months ago by ▴ 80 • written 4.5 years ago by ▴ 10
2
votes
5
replies
2.1k
views
Best way to handle samples with both single end and paired end?
RNA-Seq
updated 4.5 years ago by 90k • written 4.5 years ago by ▴ 30
1
vote
9
replies
3.5k
views
RNAseq: Modify .fasta and .gtf files to add recombinant protein sequence
reference protein modify recombinant
4.5 years ago by Pavlos • 0
0
votes
0
replies
979
views
How can I summarize Log2 Fold Change values for many genes within a treatment group?
fold-change
updated 2.2 years ago by 45k • written 4.5 years ago by ▴ 10
0
votes
1
reply
1.6k
views
Extract reads mapped within chosen intronic region from BAM file (no junctions)
bedtools RNA-seq samtools
updated 4.5 years ago by 166k • written 4.5 years ago by ▴ 10
1
vote
0
replies
768
views
ComBat before or after filtering
ComBat batchadjustment microarray
4.5 years ago by averagelife ▴ 10
1
vote
5
replies
1.9k
views
Using np to target subsampling
nonpareil coassembly metagenomics
updated 4.5 years ago by 35k • written 4.6 years ago by ▴ 10
1
vote
2
replies
1.5k
views
Picard LiftoverVcf warning - input malformated
vcf picard warning error liftover
4.5 years ago by Yuri • 0
2
votes
2
replies
1.3k
views
Forum: reporting differentially expressed genes in a global RNA-seq study
DESeq2 RNA-seq expression heatmaps transcriptomics
4.5 years ago by thomas.welch ▴ 50
0
votes
3
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2.9k
views
Installing stringr after upgrading from Ubuntu 18.04 to 20.04
18.04 20.04 stringr require error
updated 4.5 years ago by 27k • written 4.5 years ago by • 0
1
vote
4
replies
1.5k
views
WGCNA -RNAseq data- strong correlation with TIN
WGCNA TIN RNAsequencing
updated 4.5 years ago by ▴ 10 • written 4.6 years ago by • 0
1
vote
5
replies
2.5k
views
Unable to download R package
BiocManager
updated 4.5 years ago by 154k • written 4.5 years ago by • 0
0
votes
0
replies
734
views
Is there a limit on the number of query in cir_query()?
R SMILES webchem
4.5 years ago by Arindam Ghosh ▴ 550
2
votes
8
replies
5.0k
views
How to produce a heatmap by keeping the original data and a log color scale?
R heatmap ggplot2 visualization
updated 4.5 years ago by 21k • written 4.5 years ago by ▴ 270
0
votes
0
replies
1.4k
views
Memory issue with my PC when trying to convert PLINK to TreeMix
STACKS bash vcf plink treemix
4.5 years ago by hemr3 ▴ 10
0
votes
11
replies
4.1k
views
different sequencing depths for Input and IP in ChIP-Seq
depth ChIP-Seq sequencing normalisation
4.5 years ago by Genestar • 0
0
votes
1
reply
2.4k
views
Seurat - setting random seed for FindNeighbors, FindClusters
seurat clustree
4.5 years ago by bsmith030465 ▴ 250
1
vote
0
replies
679
views
Snakemake/Google-Life-Sciences aggregate funtion issue
snakemake Google-Life-Sciences
4.5 years ago by Stephan ▴ 10
6
votes
8
replies
5.9k
views
Modeling Chip-Seq Background Using Edger'S Glm Functionality?
chip-seq edger
updated 4.5 years ago by 90k • written 13.3 years ago by ★ 3.7k
0
votes
2
replies
1.1k
views
how to get the assembly number of an array with a script
ncbi
4.5 years ago by Debut ▴ 20
0
votes
2
replies
1.9k
views
How exactly does diffBind count reads?
atac-seq diffbind
updated 2.5 years ago by 45k • written 4.6 years ago by ▴ 10
1
vote
1
reply
3.1k
views
Diffbind fold difference calculation
diffbind normalization fold
updated 4.5 years ago by ★ 2.2k • written 4.6 years ago by • 0
4
votes
10
replies
3.5k
views
Beagple 5.2 phasing error
vcf beagle plink phasing
updated 4.3 years ago by 2.9k • written 4.6 years ago by ▴ 40
2
votes
2
replies
2.3k
views
Understanding PCA plot from DiffBind
diffbind pca chip-seq
updated 4.5 years ago by ★ 2.2k • written 4.6 years ago by ▴ 810
0
votes
1
reply
1.7k
views
Error executing process > 'read_clustering (1)' In NanoCLUST
NanoporeSequencing 16srrna NanoClust
updated 4.5 years ago by ★ 3.3k • written 4.5 years ago by ▴ 10
0
votes
3
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1.5k
views
i need help mouse prostata single cell data
scRNAseq porstate mouse
updated 4.5 years ago by 35k • written 4.5 years ago by • 0
1
vote
4
replies
2.6k
views
How to plot chipseq peak relative to TSS for some genes ?
chipseq R plotwithR TSS peak
updated 4.5 years ago by ★ 3.3k • written 4.5 years ago by ▴ 10
0
votes
0
replies
656
views
Transforming a straight image #1 into bent/curved form and align with bent/curved image #2.
image bent imageprocessing transform align
4.5 years ago by karolina.kowalska9696 • 0
122,200 results • Page 661 of 2444
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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: 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)?
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…
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