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122,200 results • Page 656 of 2444
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1
vote
7
replies
4.1k
views
bbduk trimmed out too many sequences
bbduk bbmap amplicon
updated 4.5 years ago by 154k • written 4.5 years ago by ▴ 30
0
votes
2
replies
2.3k
views
How to grep fasta sequence using list of IDs
grep FASTA Sequence
4.5 years ago by Kumar ▴ 170
4
votes
1
reply
1.0k
views
R script for Gene ID Mapping?
mapping R IDmapping geneID
updated 4.5 years ago by 45k • written 4.5 years ago by • 0
0
votes
2
replies
886
views
Looking for a user-friendly comparative genomics program
comparative genomics
updated 4.5 years ago by 154k • written 4.5 years ago by • 0
41
votes
20
replies
42k
views
12 follow
output TMM normalized counts with edgeR
differential expression RNA-Seq
updated 3.6 years ago by • 0 • written 7.5 years ago by ★ 1.0k
1
vote
2
replies
5.2k
views
CPM or pesudo.counts, which is the normalized counts
edgeR， CPM edgeR cpm pesudo.counts
updated 4.5 years ago by ▴ 10 • written 10.0 years ago by ▴ 40
0
votes
5
replies
2.7k
views
the fixed-effects model matrix is column rank deficient when adding a variable
voom LIMMA dream RNA rescale
updated 4.5 years ago by ▴ 310 • written 4.5 years ago by ▴ 20
4
votes
4
replies
2.7k
views
Extracting reads from BAM file based on partial read name
BAM CLI picard RNA-Seq
updated 4.5 years ago by 11k • written 4.5 years ago by ▴ 20
2
votes
3
replies
2.0k
views
Deleterious or Protective? --> CADD score >20 but Odds ratio <1
variant deleteriousness genomics
updated 4.5 years ago by ★ 90k • written 4.5 years ago by ▴ 310
1
vote
3
replies
1.2k
views
Help with record.id
pyrosetta python biopython
updated 2.7 years ago by 45k • written 4.5 years ago by • 0
3
votes
5
replies
2.3k
views
how can I turn a skinny/long data frame into a Seurat object
sparse-matrix seurat scrna-seq
4.5 years ago by glocke01 ▴ 190
2
votes
14
replies
3.1k
views
Genetic Variants in NGS analysis
variants NGS
4.5 years ago by sarastrafella.ss ▴ 20
0
votes
0
replies
718
views
Batch Effects in Multiplexed Perturbations
demultiplexing cellhashing singlecell scRNAseq
4.5 years ago by fouerghi20 ▴ 90
0
votes
2
replies
985
views
VennDiagram for differentially expressed proteins
proteomics VennDiagram
4.5 years ago by yannick.venturaavila • 0
7
votes
4
replies
7.8k
views
scvelo vs velocyto
velocyto python scvelo
updated 3.8 years ago by 9.0k • written 4.5 years ago by ▴ 20
0
votes
5
replies
2.3k
views
FeatureCounts error
RNAseq
updated 4.5 years ago by 90k • written 4.5 years ago by • 0
0
votes
1
reply
928
views
Variable name shuffles in Correlation Plot in R
R Biostatistics Corrplot Correlation
updated 4.5 years ago by 21k • written 4.5 years ago by • 0
0
votes
1
reply
727
views
Gene name according to assembly
hg38 genome assembly name hg18
updated 4.5 years ago by 154k • written 4.5 years ago by • 0
2
votes
4
replies
2.7k
views
hg18, hg19, hg38
hg38 hg19 genome assembly hg18
updated 4.5 years ago by 154k • written 4.5 years ago by • 0
1
vote
2
replies
2.8k
views
Remove sites with heterozygote excess with VCFtools
SNPs genomics VCFTools hetexcess
4.5 years ago by Konstantinos • 0
0
votes
2
replies
1.4k
views
How do commercially NIPT tests work?
NIPT NGS Defrag WisecondorX Sanefalcon
updated 4.5 years ago by ★ 3.0k • written 5.3 years ago by ▴ 20
0
votes
0
replies
646
views
Prediction model in R
Prediction R Rstudio model
4.5 years ago by yura.10.08.94.94 • 0
0
votes
0
replies
828
views
Tool/server for metal ion amino acid binding site prediction ?
proteomics database python genomics
updated 4.4 years ago by 45k • written 4.5 years ago by ▴ 120
2
votes
1
reply
1.6k
views
Error with SRA Toolkit prefetch command
timeout sra ncbi https
updated 4.5 years ago by 90k • written 4.5 years ago by ▴ 120
4
votes
3
replies
3.7k
views
Gold standard for bulk RNA-seq downsampling - number of uniquely mapped reads
uniquely RNA-seq mapping bulk downsampling
4.5 years ago by msimmer92 ▴ 310
0
votes
0
replies
601
views
Selective sweep for scaffold level reference genome
positiveselection denovo selectivesweep scaffold
4.5 years ago by Mel Kile • 0
1
vote
4
replies
1.7k
views
What is the advantage of having BAM files per sample compared to one BAM file containing all samples?
NGS BAM SNPcalling
4.5 years ago by L_to_the_m ▴ 10
1
vote
9
replies
2.1k
views
Can anyone please name this tool to make a genome map?
graphics genome
updated 4.5 years ago by 45k • written 4.5 years ago by ▴ 50
0
votes
5
replies
1.7k
views
Problem creating a reference genome
reference custom genome
4.5 years ago by lydiaiglesias • 0
1
vote
7
replies
16k
views
A problem with download SRA using SRA toolkit
SRAtoolkit NCBI SRA
updated 2.4 years ago by 45k • written 5.8 years ago by ▴ 300
0
votes
1
reply
782
views
genbank output incomplete with long feature name
biopython SeqFeature genbank SeqIO
updated 4.5 years ago by 22k • written 4.5 years ago by • 0
0
votes
2
replies
1.1k
views
extract reference and query coordinate from bam or sam file
sam bam
4.5 years ago by LMoon • 0
0
votes
0
replies
925
views
Fully online, single modules/courses in Bioinformatics and Omics Data Analysis?
university omics online academic
updated 4.4 years ago by 45k • written 4.5 years ago by • 0
0
votes
3
replies
1.6k
views
Help! Master regulator prediction from DEGs in RNA-seq
GRN transcription rna-seq DEG transcriptomics
updated 4.5 years ago by ▴ 70 • written 4.5 years ago by • 0
0
votes
0
replies
2.1k
views
Bismark to MethylKit
methylkit bismark bsseq
4.5 years ago by Arindam Ghosh ▴ 550
1
vote
1
reply
1.1k
views
Compare protein functionality between species
Genetics Comparative Proteomics
updated 4.5 years ago by ★ 30k • written 4.5 years ago by • 0
0
votes
4
replies
1.7k
views
I'm having some problems when I calculated PRS by PRsice
PRsice PRsice-2 error
4.5 years ago by dong • 0
0
votes
1
reply
1.1k
views
How to use python to align 30 kb genome to another 30kb reference, repeat 10x times ?
Alignment reference-alignment python
updated 4.5 years ago by 48k • written 4.5 years ago by ▴ 10
0
votes
0
replies
660
views
Whole Proteome Alignment
divergence alignment proteome
4.5 years ago by sentionaut • 0
8
votes
15
replies
9.2k
views
6 follow
blastn error - NCBI C++ Exception
assembly blast alignment
updated 3.7 years ago by 16k • written 4.7 years ago by ▴ 1000
0
votes
0
replies
1.1k
views
Calculating net charge of a ligand.
amber ligand Charge
4.5 years ago by Ammar Danazumi ▴ 10
10
votes
7
replies
6.0k
views
Forum: Conceptual - Do I need to justify myself if I generate more than three replicates?
statistics conceptual
4.5 years ago by c_u ▴ 530
0
votes
1
reply
1.3k
views
Merging Bam Files with Rsamtools
mergeBam Rsamtools
updated 4.5 years ago by 45k • written 4.5 years ago by • 0
0
votes
0
replies
689
views
Chipseq allelic density plot for TSS region
Chip-Seq Allelic-Chipseq Deeptools
4.5 years ago by BISEP ▴ 10
0
votes
2
replies
904
views
Identical BLAST search query producing different results?
BLAST
4.5 years ago by Felixculpa • 0
1
vote
1
reply
1.2k
views
Trimming gene coding sequence for finding TFBS
tfbs transcription binding rna-seq
4.5 years ago by greyman ▴ 190
0
votes
2
replies
1.6k
views
subset of paired end reads from bam file or fastq file of different depth
depth ShortRead samtools read
4.5 years ago by rthapa ▴ 90
2
votes
3
replies
1.9k
views
Difference between fCDS and CDS
fCDS CDS
4.5 years ago by Prashant ▴ 10
0
votes
1
reply
4.0k
views
Editing Seurat object metadata
scRNA-seq Seurat snRNA-seq
updated 4.5 years ago by ★ 1.8k • written 4.5 years ago by ▴ 30
0
votes
1
reply
843
views
Suggestion on parsing multipe alignment in fasta format
mafft multiple msa sequence clustal
updated 4.5 years ago by 21k • written 4.5 years ago by ▴ 30
122,200 results • Page 656 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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