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645
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Longest common substring between two sequences with minimum error correction
algorithm
4.4 years ago by Alex • 0
0
votes
4
replies
2.5k
views
Cellranger-arc
cellranger cellranger-arc scRNA-seq 10x
4.4 years ago by LacquerHed ▴ 30
0
votes
0
replies
1.2k
views
Job: Program Manager - Computational Biology
Computational Biosciences Biology
4.4 years ago by BerkeleyLab ▴ 70
1
vote
2
replies
1.3k
views
bcftools mpileup giving more wildtypes <*> than expected
bcftools DNA-seq mpileup
4.4 years ago by gt ▴ 30
0
votes
1
reply
843
views
Annotating CNV
gnomad Annotation
updated 4.4 years ago by 45k • written 4.4 years ago by ▴ 20
0
votes
0
replies
827
views
freebayes only picking up variants in a single contig
variant-calling DNA-seq freebayes
4.4 years ago by gt ▴ 30
2
votes
6
replies
2.4k
views
rMATS BAM file MemoryError Issue
rMATS processing BAM
4.3 years ago by saipra003 ▴ 20
0
votes
8
replies
3.1k
views
Error in DSSP Module of Biopython
Python Biopython
4.4 years ago by anasjamshed ▴ 140
0
votes
1
reply
736
views
Expression analysis of data obtained from Broad GDAC Firehouse (https://gdac.broadinstitute.org/)
gdac tcga
updated 4.4 years ago by 45k • written 4.4 years ago by • 0
2
votes
0
replies
800
views
Herald: The Biostar Herald for Tuesday, July 20, 2021
herald
4.4 years ago by Biostar 3.7k
0
votes
3
replies
2.1k
views
error related to annovar software
rsid annovar VCF SNP
4.3 years ago by rheab1230 ▴ 150
1
vote
2
replies
1.3k
views
retrieving entire genomic sequence contents of a database
genomes mining database ftp ensembl
updated 4.4 years ago by ★ 2.4k • written 4.4 years ago by • 0
0
votes
0
replies
1.0k
views
Does the normalization method affect scRNAseq data integration?
scran scuttle scRNAseq integration normalization data
4.4 years ago by joker33 ▴ 150
3
votes
8
replies
2.6k
views
Spatial transcriptomics data
scalefactor spatial
4.4 years ago by lsudupe ▴ 30
9
votes
3
replies
1.7k
views
Forum: How to manage Biostar email subscriptions?
biostars
updated 4.4 years ago by 20 • written 4.4 years ago by ▴ 890
2
votes
3
replies
1.3k
views
Exons Distribution from single cell data.
exons introns scrna
updated 4.4 years ago by 4.2k • written 4.4 years ago by • 0
103
votes
39
replies
194k
views
19 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 2.6 years ago by ▴ 180 • written 13.4 years ago by ▴ 410
1
vote
2
replies
1.4k
views
Start with MrBayes
MrBayes
updated 4.4 years ago by 5.3k • written 4.4 years ago by • 0
0
votes
0
replies
800
views
Job: Postdoc Molecular Mechanisms of Cell State Transitions - Information Management and Information Infrastructure
germany bioimaging postdoc
updated 2.7 years ago by 45k • written 4.4 years ago by • 0
0
votes
0
replies
816
views
Tool: Manticore: a software to extract the intermixed regions of subgenomes in hybrid species
mapping hybrid subgenome genomics sequencing
4.4 years ago by Matteo Schiavinato ★ 3.7k
0
votes
0
replies
631
views
E.coli Promoter sequence
Sequence Promoter E.coli RegulonDB
4.4 years ago by fufor_b • 0
3
votes
1
reply
2.1k
views
Tool: all2vcf: a tool to convert non-standard variant outputs (mummer. bcftools isec) to VCF
mummer isec variant bcftools VCF
updated 3.1 years ago by • 0 • written 4.4 years ago by ★ 3.7k
0
votes
2
replies
1.1k
views
Does PLINK2 have the function of batch processing ?
batch processing plink2
updated 4.4 years ago by ★ 2.2k • written 4.4 years ago by • 0
9
votes
10
replies
8.7k
views
8 follow
Which method is the best for using in "dba.count" in Diffbind R package
ChIP-Seq diffbind
updated 2.0 years ago by ★ 2.2k • written 6.2 years ago by ▴ 120
0
votes
0
replies
902
views
GFF/GTF: how to translate CDS genomic coordinates to protein coordinates
GTF GFF3
updated 4.4 years ago by 9.3k • written 4.4 years ago by ★ 1.2k
3
votes
5
replies
2.7k
views
Does Last aligner only outputs the mapped reads to a bam file ?
assembly alignment sequencing next-gen genome
updated 4.4 years ago by • 0 • written 7.3 years ago by ▴ 210
0
votes
0
replies
1.7k
views
Tool: Handy online tool for genomic analysis and data visualization - Part I
NGS Sequencing
updated 2.7 years ago by 45k • written 4.4 years ago by ▴ 520
0
votes
1
reply
1.5k
views
determination of alternate splicing events from assembled transcripts
rna-seq
updated 4.4 years ago by ▴ 590 • written 7.4 years ago by ▴ 110
1
vote
1
reply
1.1k
views
GATK VQSR for human WGS
WGS alignment genome
updated 4.3 years ago by ▴ 270 • written 4.4 years ago by ▴ 120
0
votes
0
replies
1.3k
views
GATK MarkDuplicates Metrix issues
Markduplicates Picard RNASeq
4.4 years ago by aka ▴ 10
1
vote
2
replies
4.2k
views
bcftools stats output file specification?
bcftools stats
4.4 years ago by Jordi ▴ 60
0
votes
1
reply
982
views
Whole genome sequencing.
NGS
updated 4.4 years ago by ▴ 590 • written 4.4 years ago by • 0
3
votes
8
replies
2.3k
views
Can someone suggest any python script or any script so that I can make modification in my excel sheets or text file ?
code python
updated 4.4 years ago by 90k • written 4.4 years ago by • 0
0
votes
0
replies
912
views
How do I create a heat map (ASVs) with corresponding taxonomic rank with ggplot2?
microbiome heatmap
4.4 years ago by neokao • 0
1
vote
5
replies
5.7k
views
Error in `$<-.data.frame`(`*tmp*`, "feature", value = XXX) replacement has YYY rows, data has 0
R
updated 4.4 years ago by 45k • written 4.4 years ago by ▴ 110
1
vote
3
replies
1.5k
views
Featurecount mapping is less
Featurecount STAR RNAseq
4.4 years ago by vinishavvenugopal ▴ 30
0
votes
0
replies
979
views
Gini Index Box plot
RNA-Seq TCR R Seurat 10x
4.4 years ago by roberts ▴ 60
0
votes
0
replies
810
views
linking BRENDA ligands to InChlKey
InChlKey CHEBI enzyme BRENDA
4.4 years ago by bioguy ▴ 50
0
votes
2
replies
1.8k
views
Gblocks file not opened error
Conserved MSA regions
updated 4.4 years ago by ▴ 460 • written 4.4 years ago by • 0
1
vote
4
replies
2.2k
views
Reading and normalizing raw data on R
GEO normalization R
4.4 years ago by Fate • 0
1
vote
2
replies
1.1k
views
Gene annotations of HLA-A genes
genes A11 HLA-A2 annotation genome A3 gene
4.4 years ago by zhang.wen81 • 0
0
votes
0
replies
819
views
HLA typing of SCC152 cell lines
copy cell number lines SCC152 RNA-seq E7 typing HLA
4.4 years ago by zhang.wen81 • 0
0
votes
0
replies
1.2k
views
HLA haplotypes VCF
HLA Haplotype VCF
4.4 years ago by rubic ▴ 270
2
votes
3
replies
1.3k
views
Are there risks to use a GRCh38 gtf and a hg19 fa in alignment?
RNASeq
updated 4.4 years ago by 15k • written 4.4 years ago by ▴ 90
2
votes
2
replies
2.9k
views
BWA error: [bwa_idx_build] fail to open file 'ref.fa' : No such file or directory
BWA
updated 4.4 years ago by 15k • written 4.4 years ago by • 0
0
votes
0
replies
1.8k
views
Job: Looking for Intern, Junior positions in bioinformatics/computational biology
oncology biostatistics R
updated 4.4 years ago by 21k • written 4.4 years ago by • 0
0
votes
1
reply
813
views
inexpensive method to detect SNPs in entire bacterial genomes
bacteria SNPs RFLP genome
updated 4.4 years ago by ★ 30k • written 4.4 years ago by ▴ 10
25
votes
5
replies
10k
views
Conda, bioconda, anaconda, are they different?
Conda anaconda bioconductor bioconda
4.4 years ago by hamid.gaikani ▴ 80
1
vote
2
replies
1.3k
views
Precomputed MSAs for human proteome
proteome msa
4.4 years ago by david.f.stein ▴ 10
1
vote
3
replies
3.1k
views
How to perform logistic regression (with option “firth-fallback”) in Plink2
plink
updated 4.4 years ago by 11k • written 4.4 years ago by ▴ 50
122,200 results • Page 616 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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