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122,198 results • Page 642 of 2444
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3
votes
3
replies
3.4k
views
How to connect HLA alleles with rsID?
rsid
updated 4.5 years ago by • 0 • written 4.6 years ago by ▴ 380
4
votes
5
replies
3.1k
views
Command to parse mummer coords file
mummer nucmer
updated 4.5 years ago by ▴ 20 • written 6.0 years ago by ▴ 80
0
votes
7
replies
3.4k
views
Malformed BED entry at line 5. Start Coordinate detected that is < 0. Exiting.
unibind BED
updated 4.5 years ago by 21k • written 4.5 years ago by • 0
5
votes
7
replies
5.1k
views
Converting LogCPM to raw counts for DESEQ2
rna-seq
updated 21 months ago by ★ 8.6k • written 4.5 years ago by ▴ 70
0
votes
0
replies
611
views
Realign previous alignments
mafft alignment
4.5 years ago by QLFblaireau ▴ 30
1
vote
8
replies
2.1k
views
Unexpected blastx results
blast blastx
4.0 years ago by langziv ▴ 70
1
vote
1
reply
1.6k
views
Filtering out relevant Gene-fusions
Gene fusion filtering
updated 4.5 years ago by 5.9k • written 4.5 years ago by ▴ 30
0
votes
0
replies
1.2k
views
Hi-C merged files
Hi-C .hic
4.5 years ago by Oleczkaff • 0
1
vote
15
replies
5.9k
views
bcftools filter by protein prediction
bcftools
updated 4.5 years ago by ▴ 480 • written 4.5 years ago by ▴ 30
19
votes
6
replies
19k
views
6 follow
How to trim Nanopore reads. Please suggest a tool.
Nanopore MinIONQC ONT
updated 4.5 years ago by 48k • written 5.9 years ago by ▴ 80
0
votes
1
reply
776
views
Screening for high-impact mutations from WES-based variant calling and annotation
Variant screening
updated 4.5 years ago by 166k • written 4.5 years ago by ▴ 30
3
votes
6
replies
2.6k
views
genome assembly - size of gaps
PBJelly assembly_genome linked_reads gaps
updated 4.5 years ago by 16k • written 4.5 years ago by ▴ 20
0
votes
7
replies
2.2k
views
Counting reads with feature counts.
Genomics
4.5 years ago by aranyak111 • 0
1
vote
4
replies
1.5k
views
common coordinates from 10 files
coordinates common
4.5 years ago by K ▴ 10
0
votes
2
replies
1.8k
views
readFilesCommand not working
readFilesCommand rnaseq STAR
4.5 years ago by vinishavvenugopal ▴ 30
0
votes
1
reply
896
views
How to calculate Oncotype score and Mammaprint score from an RNAseq
Manmaprint Oncotype
updated 4.5 years ago by 45k • written 4.5 years ago by • 0
1
vote
4
replies
3.1k
views
Gene expression RNASeq
DESEQ2 RNAseq
updated 4.5 years ago by ★ 3.1k • written 4.5 years ago by ▴ 30
3
votes
7
replies
2.6k
views
Clarification regarding VCF fields (file format)
mutation VCF SNPs format
updated 4.5 years ago by ▴ 160 • written 4.5 years ago by 7.6k
4
votes
3
replies
2.4k
views
Job: Senior Bioinformatics Scientist
Senior-Scientist Geltor
updated 4.4 years ago by 45k • written 4.5 years ago by ▴ 10
0
votes
4
replies
3.8k
views
Convert MSTRG gene IDs to real one?
Gene MSTRG Stringtie
updated 4.5 years ago by 15k • written 4.5 years ago by • 0
2
votes
2
replies
1.2k
views
Does spades/metaspades normally having missing nodes?
metaspades spades
4.5 years ago by DNAngel ▴ 260
2
votes
9
replies
3.9k
views
RNAseq: units (TPM +0.001).
TPM ARNseq
updated 3.3 years ago by ★ 1.2k • written 4.5 years ago by • 0
0
votes
5
replies
4.2k
views
retrieve_pdb_file from Bio.PDB.PDBList creates .ent files, not .pdb
biopython bio.pdb pyrosetta PDBList rmsd
updated 4.4 years ago by ★ 30k • written 4.5 years ago by • 0
5
votes
0
replies
1.1k
views
Herald: The Biostar Herald for Tuesday, June 08, 2021
herald
updated 4.5 years ago by 103k • written 4.5 years ago by 3.7k
8
votes
8
replies
2.7k
views
Find genes overlapping intervals in R and keep the original Intervals
bedtools annotations R genes
updated 4.5 years ago by 45k • written 4.5 years ago by ▴ 40
1
vote
5
replies
2.7k
views
allele frequency from different read depths
allele depth frequency vcf read
updated 4.5 years ago by ▴ 430 • written 4.5 years ago by ▴ 90
0
votes
2
replies
1.3k
views
Building a phylogenetic tree from different ortholog groups
COGs phylogenetics msa
4.5 years ago by timothy.kirkwood ▴ 140
0
votes
6
replies
2.0k
views
Query regarding Differentially Expressed Genes Network analysis.
Network Analysis STRING
updated 4.4 years ago by 45k • written 4.5 years ago by • 0
0
votes
0
replies
1.1k
views
Read trimming in BS-Seq
Methylation BS-Seq Bismark WGBS
4.5 years ago by Arindam Ghosh ▴ 550
0
votes
0
replies
982
views
Lastz output interpretation - only entries from positive strand
genome pairwise alignment lastz
4.5 years ago by manaswwm ▴ 570
0
votes
5
replies
2.2k
views
segfault in ADMIXTURE
software error
updated 4.5 years ago by ▴ 820 • written 4.8 years ago by • 0
0
votes
0
replies
671
views
GPSPROT image/network download with script
GPSPROT
4.5 years ago by Shicheng Guo ★ 9.6k
2
votes
4
replies
2.0k
views
Merge replicate fastq files of the same sample together?
fastq RNA-seq
4.5 years ago by foxiw ▴ 10
0
votes
3
replies
1.3k
views
Can you predict the size of a BAM file based on the fasta?
storage mapping bam
updated 4.5 years ago by ★ 90k • written 4.5 years ago by ▴ 130
0
votes
0
replies
1.3k
views
Calculate distances from multi fasta alignment considering ambiguous bases as different
distances msa python unix
4.5 years ago by Gon ▴ 10
4
votes
3
replies
3.2k
views
How to create a subset from a Nanopore fast5 file?
nanopore fast5 ont
4.5 years ago by shelkmike ★ 1.8k
0
votes
0
replies
1.0k
views
extract transcripts with particular class code in Cuff/GffCompare
GffCompare Class CuffCompare code RNA-Seq
4.5 years ago by SKY ▴ 60
5
votes
3
replies
3.9k
views
Purpose of bamCoverage RPKM normalization method
rpkm bamCoverage
updated 4.5 years ago by 90k • written 4.5 years ago by ▴ 390
7
votes
3
replies
5.8k
views
error bowtie2-align exited with value 134
fastq bowtie2
updated 4.5 years ago by 90k • written 4.5 years ago by ★ 1.3k
1
vote
1
reply
1.0k
views
problem with contrastive principal component analysis (cPCA)
scPCA cPCA
updated 4.5 years ago by 90k • written 4.5 years ago by ▴ 260
0
votes
0
replies
811
views
Map BED12 file exon coordinates between species using UCSC liftOver
software problem liftOver
4.5 years ago by celebiration8 ▴ 10
0
votes
2
replies
1.1k
views
RNA-Microarray-Data-Analysis
Microarray Expression
updated 4.5 years ago by ▴ 880 • written 4.5 years ago by ▴ 40
0
votes
3
replies
1.3k
views
adding gene symbol to bed file
gene-symbol bed
updated 2.7 years ago by 45k • written 4.5 years ago by ▴ 40
0
votes
1
reply
1.2k
views
The huge difference in results draft assembly between Canu with Flya
Nanopore ONT Flya Canu
updated 4.5 years ago by 8.1k • written 4.5 years ago by ▴ 100
4
votes
9
replies
3.2k
views
extracting ensembl gene id or entrez gene id from a gene annotation file for BINGO app of cytoscape
BINGO analysis RNA-seq R GO
updated 4.4 years ago by ★ 1.1k • written 4.5 years ago by ▴ 30
1
vote
0
replies
1.8k
views
Tutorial: How to: make Camellia sinensis var. sinensis (black tea) custom annotation files for BINGO Cytoscape
bingo cytoscape
4.5 years ago by Pratik ★ 1.1k
3
votes
5
replies
2.5k
views
Change format of counts of single cell RNA-seq data from csv to mtx format from synapse.org
single RNA-seq cell
4.5 years ago by ali_karimnezhad ▴ 20
1
vote
2
replies
1.9k
views
R package DiffBind -- Error: No sites have activity greater than minMaxval
DiffBind
4.5 years ago by alexmondaini ▴ 20
0
votes
2
replies
1.2k
views
Best method of integrative analysis for GWAS and differential expression data
GWAS
4.5 years ago by Shicheng Guo ★ 9.6k
2
votes
7
replies
6.5k
views
6 follow
How to remove samples with no genotypes from vcf
VCF
updated 3.1 years ago by ▴ 50 • written 4.5 years ago by ▴ 510
122,198 results • Page 642 of 2444
Recent Votes
Answer: Midpoint rooting IQTREE newick file moves node support around
Answer: Subsetting before QC in Spatial Transcriptomics
Answer: Feature Counts vs Salmon quantification
Comment: Feature Counts vs Salmon quantification
Answer: Can i use orthofinder for small protein datasets and not full proteome?
Comment: Comparison of different RNAseq data sets
Comment: ID unifiying across different datasets
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Recent Replies
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(…
Answer: Finding Sentrix ID in HM450K arrays by yura.grabovska ▴ 890
``` ##Using R, illuminaio from Bioconductor library(illuminaio) temp.idat <- readIDAT(file = "200379120087_R02C02_Grn.idat") tem…
Comment: Can i use orthofinder for small protein datasets and not full proteome? by michael.ante ★ 4.0k
Do you want to compare them by sequence or by function? For the later, you can use e.g. InterProScan, KoFamScan.
Answer: Can i use orthofinder for small protein datasets and not full proteome? by dthorbur ★ 3.2k
If you're just using the tool for clustering purposes, I think OrthoFinder might be a little clunky and would recommend using something lik…
Comment: ID unifiying across different datasets by zizigolu ★ 4.4k
Thank you; The problem is let's say in the protein ID column I see `Q5VTE0;P68104;Q05639` here I am sure I should get which `ENSG` for eac…
Comment: How to improving 2-Nucleotide RNA-seq Mapping Accuracy by 2411110159 • 0
Since we do not have real data yet, I tried to simulate this using strand-specific RNA bisulfite-seq reads (C to T). Read1 corresponds to t…
Comment: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies by 2411110159 • 0
Very helpful!
Comment: direct RNA long-reads alignment against reference genome by frarodmar17 • 0
Okay, thanks! I removed reads.fa and I used the index created with minimap2 in .mmi format. Is this correct?
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