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122,201 results • Page 663 of 2445
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basic pathways analysis - bacteria genome
microbial pathway
4.6 years ago by biobiu ▴ 150
0
votes
1
reply
1.8k
views
edgeR differential expression analysis - switch intercept coefficient
logFC rnaseq edgeR
4.6 years ago by Al Murphy ▴ 40
0
votes
0
replies
696
views
Gene function and network analysis pathway and GO
Geneontology Pathway Reactome KEGG
4.6 years ago by BISEP ▴ 10
0
votes
2
replies
1.4k
views
Why does FragGeneScan, a metagenome gene prediction tool, use a 6-periodic HMM?
gene prediction Markov-model metagenome
updated 4.6 years ago by 21k • written 4.6 years ago by • 0
0
votes
0
replies
722
views
microRNA attachment site database
miRNA lncRNA
4.6 years ago by Amir.Asgary ▴ 30
1
vote
1
reply
1.3k
views
Error in loading R package maEndToEnd using BiocManager
R biconductor biocmanager rstudio
updated 4.6 years ago by ★ 90k • written 4.6 years ago by ▴ 20
0
votes
1
reply
1.4k
views
Pysam and CRAM file
cram pysam samtools
updated 4.5 years ago by ★ 1.3k • written 4.6 years ago by ▴ 30
0
votes
4
replies
3.0k
views
7 follow
Using R Studio on Cloud
Single Cell RNA-Seq R rstudio
updated 4.5 years ago by ▴ 590 • written 5.4 years ago by ▴ 120
2
votes
3
replies
1.3k
views
DEseq2 AND edgeR
DEseq2
updated 4.6 years ago by ★ 8.6k • written 4.6 years ago by ▴ 10
0
votes
1
reply
1.2k
views
Different answers code
code output
updated 4.6 years ago by 16k • written 4.6 years ago by • 0
1
vote
2
replies
2.8k
views
Problem with obitools (obiconvert a simple fasta to ecopcr)
obiconvert ecopcr obitools
updated 3.8 years ago by • 0 • written 4.6 years ago by ▴ 10
2
votes
2
replies
1.2k
views
Forum: https://biostar.slack.com account
ngs
updated 4.6 years ago by 154k • written 4.6 years ago by ▴ 30
1
vote
5
replies
1.7k
views
convert tabular data to fasta
linux fasta
updated 2.4 years ago by 45k • written 4.6 years ago by • 0
0
votes
0
replies
829
views
NIPTmer testing
NIPT
4.6 years ago by smrutimayipanda ▴ 20
2
votes
8
replies
2.4k
views
Retrieve Vectorbase ID from NCBI ID [Solved]
refseq identifier vectorbase database
4.6 years ago by benoahb ▴ 40
2
votes
5
replies
1.9k
views
VCF filtering
vcf SNPfiltering genotype
updated 4.6 years ago by 14k • written 4.6 years ago by ▴ 50
0
votes
3
replies
1.8k
views
How to create a MD plot (plotMD() function) using DESEq2 results?
deseq2 mdplot edger
updated 4.6 years ago by 90k • written 4.6 years ago by • 0
0
votes
3
replies
1.9k
views
How can I get three letter organism code for cavia porcellus?
GO three KEGG
updated 4.6 years ago by 7.6k • written 4.6 years ago by ▴ 80
0
votes
0
replies
1.0k
views
Problems associated with handling of missing characters on bcftools consensus and vcf-consensus
missingcharacters bcftools vcf-consensus
4.6 years ago by Harsha Kumar • 0
2
votes
3
replies
2.2k
views
Comparing fastq files
bam reads sequencing fastq align
updated 4.6 years ago by 14k • written 4.6 years ago by • 0
3
votes
2
replies
6.7k
views
How to add labels to a Seurat object, matching the barcodes?
R seurat
updated 4.4 years ago by • 0 • written 4.6 years ago by ▴ 10
0
votes
4
replies
1.7k
views
bioinformatic sequence interpretation
interpetation sequence
updated 4.6 years ago by ★ 1.8k • written 4.6 years ago by • 0
0
votes
1
reply
1.9k
views
Job: Biostatistics/Bioinformatics Research Scientist at UNC Charlotte
R pathview singlecellRNA-Seq statistics
4.6 years ago by bigmawen ▴ 440
0
votes
0
replies
1.0k
views
TSS file format - loadPromoters.pl in Homer
TSS Homer
4.6 years ago by boczniak767 ▴ 880
4
votes
0
replies
1.2k
views
Allele Frequencies in Kaviar vs. gnomAD
gnomAD allele-frequency kaviar
4.6 years ago by ariel ▴ 250
0
votes
1
reply
1.0k
views
How to calculate median peptide intensity of each protein in mass-spec dataset in R
bioconductor r transcriptomics proteomics
updated 4.6 years ago by 90k • written 4.6 years ago by • 0
0
votes
1
reply
1.2k
views
How to extract regions from abed file based on variants in vcf file
vcf bed vcftools
updated 4.6 years ago by 36k • written 4.6 years ago by ▴ 110
2
votes
2
replies
2.4k
views
Issue with NCBI esearch
ncbi esearch edirect
4.6 years ago by yp19 ▴ 70
0
votes
0
replies
771
views
GATK HaplotypeCaller only seeing 1 thread GCP
gcp gatk kubernetes snakemake
updated 4.6 years ago by 154k • written 4.6 years ago by ▴ 10
0
votes
3
replies
2.7k
views
Possible to remove .nosex IDs in Plink1.9
--allow-no-sex --must-have-sex plink1.9
4.6 years ago by salman_96 ▴ 70
0
votes
2
replies
1.1k
views
How to split local blast database in python class
python blast database
4.6 years ago by Maria • 0
4
votes
4
replies
8.0k
views
Find count of reads in BAM file that fall within BED region
bedtools BAM overlap BED
updated 4.6 years ago by 166k • written 4.6 years ago by ▴ 100
1
vote
5
replies
2.3k
views
Locating BLAST data needed by netsurfp
blast netsurfp
updated 4.5 years ago by 154k • written 4.6 years ago by ▴ 10
0
votes
3
replies
1.7k
views
Sequencing depth and raw counts
gene ngs transcriptomics sequencing
updated 4.5 years ago by 13k • written 4.6 years ago by ▴ 320
0
votes
1
reply
1.4k
views
Job: Multiple Opportunities in Microbial Computational Biology at Lanzatech
Sequence_Analsyis Metagenomics Modeling AI Systems
updated 4.6 years ago by 21k • written 4.6 years ago by • 0
1
vote
3
replies
1.9k
views
quering publicaly available data sets of RNA-seq and constructing a Kaplan Meier plot
Meier plot Kaplan TCGA cBioportal clinical GDC
updated 4.6 years ago by 7.6k • written 4.6 years ago by • 0
9
votes
10
replies
17k
views
8 follow
Fasta file and GTF file for STAR alignment
STAR ensembl
updated 2.8 years ago by ▴ 140 • written 7.5 years ago by ▴ 80
2
votes
2
replies
1.4k
views
Genbank accession number + nucleotide position to genomic coordinates
genbank genome number accession
updated 4.6 years ago by 154k • written 4.6 years ago by ★ 2.1k
6
votes
11
replies
3.7k
views
7 follow
How do I interpret a 200bp reduction of coverage in a gene exon?
read-depth coverage golden-helix bam
updated 2.7 years ago by 45k • written 4.6 years ago by • 0
0
votes
4
replies
1.7k
views
Convert phased vcf to Chromosome/scaffold + Tag Haplotype Matrix
vcf phased haplotypes shapeit bcftools
4.6 years ago by QPaps04 ▴ 160
0
votes
0
replies
726
views
Changes in the definition of resistant, intermediate, and susceptible bacteria
bacteria EUCAST antibiotic_resistance antibiotic
4.6 years ago by Researcher ▴ 20
10
votes
4
replies
4.9k
views
UMI deduplication after common sequence (QIAseq miRNA Library Kit)
RNA-seq miRNA UMI
updated 4.6 years ago by 154k • written 4.6 years ago by ▴ 30
0
votes
0
replies
733
views
Local database connection and remote download error using curatedTCGAData
TCGA bioconductor r ExperimentHub
4.5 years ago by robjohn70000 ▴ 160
0
votes
0
replies
1.2k
views
Could bcftools output GQ for homozygous REF call?
samtools gvcf genotype bcftools
4.6 years ago by wang.yiguan ▴ 10
0
votes
0
replies
870
views
MAF and LD matching SNP list
variants snpsnap control
4.6 years ago by gokberk ▴ 90
0
votes
0
replies
732
views
Resistance breakpoints from CLSI for antibiotic resistance
resistance_cutoffs antibiotic CLSI e._coli
4.6 years ago by Researcher ▴ 20
0
votes
0
replies
581
views
How to generate plot with 2 opposite y axis with different scaling?
R Plot
4.6 years ago by xqyn ▴ 60
9
votes
11
replies
4.7k
views
How to filter a vcf file based on genotype of first two samples
vcf genotype filter
updated 4.6 years ago by 14k • written 4.6 years ago by ▴ 110
1
vote
4
replies
2.1k
views
Download whole 1000 genome phase 3 for LD clumping
genomic plink
updated 4.4 years ago by 45k • written 4.6 years ago by ▴ 10
5
votes
3
replies
2.4k
views
Problem connecting web in PLINK
GWAS PLINK
updated 11 months ago by • 0 • written 4.6 years ago by ▴ 40
122,201 results • Page 663 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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