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122,200 results • Page 617 of 2444
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2
votes
1
reply
1.7k
views
Understanding the number of intersection in bedtools jaccard
bedtools comparison vcf snps
updated 4.4 years ago by 22k • written 4.4 years ago by ▴ 30
3
votes
3
replies
2.6k
views
homebrew Vs bioconda
homebrew bioconductor
updated 4.4 years ago by 9.3k • written 4.4 years ago by ▴ 80
1
vote
5
replies
1.7k
views
Filter unique values over columns from a dataframe in R
gene R
updated 4.4 years ago by 21k • written 4.4 years ago by ▴ 10
14
votes
18
replies
9.2k
views
Python script to calculate properties of amino acids
python
updated 3.0 years ago by 45k • written 4.4 years ago by ▴ 140
6
votes
4
replies
3.0k
views
How can read-count from BAM file be greater than than from fastq file?
rna-seq
updated 4.4 years ago by 22k • written 4.4 years ago by ▴ 530
2
votes
3
replies
1.4k
views
Generate consensus from a BAM file to each of the variants
bam coinfection consensus ivar
4.4 years ago by fhsantanna ▴ 620
4
votes
4
replies
2.6k
views
RNA variant calling, aligned with HiSat2
hisat2 gatk splitncigar
4.4 years ago by OhHiImNewHere ▴ 10
1
vote
2
replies
1.3k
views
How to pick top 50 the most abundant pathways?
pathways abundant
4.4 years ago by arshad1292 ▴ 110
1
vote
1
reply
1.2k
views
News: Online Course - A Practical Introduction to NGS Data Analysis (September 15-17, 2021)
workshop DNAseq RNAseq
updated 4.4 years ago by ▴ 590 • written 4.4 years ago by 11k
2
votes
3
replies
1.9k
views
snakemake error: MissingInputException
pipeline snakemake
updated 4.4 years ago by ▴ 580 • written 4.4 years ago by • 0
0
votes
1
reply
919
views
Adding fakes genotypes columns to a vcf file
bcftools vcftools vcf genotype
updated 4.4 years ago by ▴ 480 • written 4.4 years ago by • 0
0
votes
0
replies
697
views
metagenemark model file
metagenemark metagenome prokaryote
4.4 years ago by bioinfo_ga ▴ 70
5
votes
6
replies
2.3k
views
Any Tools to calculate specific gene coverage from BAM file?
Coverage
4.3 years ago by koay • 0
45
votes
2
replies
39k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa
updated 2.8 years ago by 45k • written 13.6 years ago by ▴ 540
0
votes
1
reply
1.1k
views
Association analysis with SNP
association WGS GWAS SNP WES
updated 4.4 years ago by ▴ 1000 • written 4.4 years ago by ▴ 40
1
vote
2
replies
1.5k
views
Batch verify hairpin structure
miRNA
4.3 years ago by 153348734 • 0
1
vote
1
reply
1.9k
views
ChEMBL ID to Ensembl ID
ChEMBL Ensembl
updated 4.4 years ago by ★ 1.1k • written 4.4 years ago by ★ 9.6k
9
votes
10
replies
3.0k
views
How to use Poisson distribution to get meaningful expression counts?
statistics rna-seq
updated 4.4 years ago by 22k • written 4.4 years ago by ▴ 530
3
votes
2
replies
1.2k
views
Add text to fasta header based in a list
fasta header R bash
updated 4.4 years ago by 21k • written 4.4 years ago by ▴ 30
1
vote
2
replies
1.7k
views
snpEff ERROR_CHROMOSOME_NOT_FOUND GRCh37.75 genome
annotaion vcf genomics variant snpEff
4.4 years ago by rbioinfo ▴ 40
1
vote
5
replies
1.8k
views
HaplotypeCaller doesn't output the VCF
BAM VCF GATK HaplotypeCaller
updated 4.4 years ago by • 0 • written 4.4 years ago by ▴ 10
0
votes
3
replies
2.3k
views
conversion of case_ids to file_ids TCGA data
TCGA case_ids conversion
updated 4.4 years ago by • 0 • written 6.5 years ago by ▴ 530
1
vote
0
replies
902
views
Kaplan Meier Plotter and Competing risk model survival analysis
Competing risk anaylsis model Kaplan-Meier
4.4 years ago by aronno.geb ▴ 10
0
votes
0
replies
1.3k
views
Stringtie error : discarding overlapping duplicate miRNA feature
miRNA stringtie
updated 17 months ago by 45k • written 4.4 years ago by ▴ 30
0
votes
0
replies
573
views
Germline calling with differents sample source
WGS alignment genome
4.4 years ago by quentin54520 ▴ 120
7
votes
3
replies
3.0k
views
snakemake to merge bams from multiple samples
snakemake
updated 4.4 years ago by ▴ 580 • written 4.4 years ago by ▴ 260
1
vote
2
replies
1.5k
views
Bioinformatic tool for acinetobacter plasmids
plasmidseeker plasmidfinder plasmid
4.4 years ago by blur ▴ 280
0
votes
2
replies
1.3k
views
From case uuid to specific file uuid
TCGA GDC
4.4 years ago by adebola.1 • 0
1
vote
1
reply
1.8k
views
Fastest way to use pysam view in order to get the reads in different regions
pysam_view samtools pysam bam optimisation
updated 4.4 years ago by ▴ 580 • written 4.4 years ago by ▴ 30
0
votes
2
replies
996
views
RNA without replication 2
RNA-Seq
updated 3.4 years ago by 45k • written 4.4 years ago by ▴ 10
1
vote
8
replies
2.4k
views
RNA without replication
RNA-Seq
updated 3.4 years ago by 45k • written 4.4 years ago by ▴ 10
5
votes
5
replies
4.1k
views
Adapter trimming
Trimmomatic Fastqc Adapter
updated 4.4 years ago by ▴ 460 • written 4.4 years ago by • 0
2
votes
1
reply
939
views
why is important to identify genetic risk variants?
genetic risk variants
updated 4.4 years ago by ★ 90k • written 4.4 years ago by ▴ 10
0
votes
0
replies
656
views
3D protein modeling and Docking studies
modeling 3D- Docking
4.4 years ago by aronno.geb ▴ 10
0
votes
0
replies
562
views
Constraint based modelling, Flux Balance analysis
analysis Flux Balance
4.4 years ago by ShiwangiW • 0
3
votes
2
replies
4.4k
views
Why ATAC-seq/CUT&RUN need paired-end sequencing?
HiC sequencing
updated 4.4 years ago by • 0 • written 6.4 years ago by • 0
1
vote
3
replies
2.0k
views
Using BiomaRt returns to get entrez gene ids returns an error. Why is this happening?
BiomaRt R
4.4 years ago by peter.berry5 ▴ 60
1
vote
6
replies
2.7k
views
mapper.pl gives empty output
miRDeep2 Bowtie mapper.pl
updated 4.4 years ago by ▴ 590 • written 4.4 years ago by ▴ 30
1
vote
4
replies
2.3k
views
Abnormal fastq lines
fastq-file-error SRR-flile mapping-error
updated 4.4 years ago by 154k • written 4.4 years ago by ▴ 110
0
votes
0
replies
780
views
Error : no alignment column
Phylip python Vcf Iqtree
4.4 years ago by Kagisoralph • 0
8
votes
6
replies
2.5k
views
Use bioinformatics tool in iphone 7
megax chimera Android modeler
updated 3.0 years ago by 45k • written 4.4 years ago by ▴ 140
5
votes
3
replies
4.1k
views
How to loop to use trimmomatic for multiple fastq files?
linux trimmomatic
updated 4.4 years ago by ▴ 460 • written 4.4 years ago by ▴ 50
0
votes
2
replies
1.2k
views
NGS QC metrics ( comparison )
QC metrics NGS
4.4 years ago by jovecit478 • 0
2
votes
1
reply
1.6k
views
How do you update plink bim file to remove 'chr' string?
plink
updated 4.4 years ago by 11k • written 4.4 years ago by ▴ 50
1
vote
3
replies
1.7k
views
Troubleshooting Missing_Read_Group and Mismatch_Flag_Mate Errors
Picard BWA
updated 4.4 years ago by 154k • written 4.4 years ago by ▴ 70
0
votes
0
replies
605
views
Fine Mapping Program (FOCUS) Stalling on Chromosome 6
FOCUS mapping fine
updated 4.4 years ago by 45k • written 4.4 years ago by • 0
0
votes
1
reply
1.4k
views
How to conduct a genomic SEM with GxE term and term for G effect on E?
sem gwsem gwas GxE genomic
updated 4.4 years ago by ▴ 940 • written 4.4 years ago by ▴ 10
0
votes
0
replies
724
views
Correct way of calculating Titv ratios for QC
QC titv WES ratio
4.4 years ago by diana.cornejo • 0
2
votes
5
replies
2.6k
views
RNA sequence analyzing data using R after DESeq2 (illumina)
RNA-Seq
updated 3.4 years ago by 45k • written 4.4 years ago by ▴ 10
0
votes
3
replies
4.7k
views
How to calculate R2 from GWAS summary statistics?
GWAS MLM LMM chi-square R2
4.4 years ago by okiedokie1208 ▴ 40
122,200 results • Page 617 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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