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Analysis of CRISPR screening with very strong positive selection
MAGeCK CRISPR
4.5 years ago by di4mond • 0
0
votes
1
reply
1.7k
views
Build phylogenetic tree with alignment file
nwk phylogenetic aln alignment
updated 4.5 years ago by 56k • written 4.5 years ago by ▴ 70
0
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0
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1.2k
views
Job: PhD scholarship in bioinformatics in Rostock (Baltic Coast), Germany
aging nutrition
updated 4.4 years ago by 45k • written 4.5 years ago by • 0
0
votes
1
reply
1.3k
views
How do I correctly add a plasmid sequence with multiple genes to a gtf as well as fasta file?
gtf fasta plasmid
updated 4.5 years ago by ▴ 160 • written 4.5 years ago by • 0
7
votes
4
replies
2.3k
views
Up to date bulk RNA-seq Quality Control tools?
QC RNA-seq
4.5 years ago by Pratik ★ 1.1k
0
votes
4
replies
1.4k
views
AWS EC2 connection with External hard drive (portable hard drive)
EC2 AWS
updated 4.4 years ago by 45k • written 4.5 years ago by • 0
0
votes
1
reply
1.2k
views
samtools mpileup: error CRC32 failure
sequencing SNP genome next-gen gene
updated 4.5 years ago by 166k • written 4.5 years ago by ▴ 10
1
vote
1
reply
859
views
Finding if genes present in a gene list intersect genomic intervals
bed encode gene
4.0 years ago by alexmondaini ▴ 20
0
votes
1
reply
2.2k
views
Packages installation: Permission denied
bioconductor R packages
updated 4.5 years ago by 12k • written 4.5 years ago by ▴ 10
1
vote
2
replies
971
views
Split a sam file by chromosome
CNVs NGS PRISM
updated 4.5 years ago by 154k • written 4.5 years ago by ▴ 20
4
votes
6
replies
2.9k
views
Trim bam file reads to the same length
RNA-Seq genome sequencing next-gen
updated 4.5 years ago by 9.3k • written 5.8 years ago by ▴ 40
0
votes
0
replies
821
views
Job: Postdoc position on Modeling Gene Disruptions involved in Speech and Language Impairment in Human Neurons
transcriptomics single epigenetics cell
4.5 years ago by pancakeplant ▴ 10
1
vote
2
replies
2.7k
views
Salmon quant produced an error
Salmon Linux
updated 22 months ago by ▴ 10 • written 4.5 years ago by ▴ 30
2
votes
1
reply
1.1k
views
effects of posttranslational protein modifications database?
post-translational-modification protein
updated 15 months ago by 45k • written 4.5 years ago by ▴ 30
0
votes
1
reply
1.7k
views
bcftools add AD column
ad bcftools vcf
updated 4.5 years ago by 12k • written 4.5 years ago by • 0
1
vote
5
replies
2.6k
views
Trimmomatic: Unknown trimmer error
fastq trimmomatic RNA-seq
4.5 years ago by foxiw ▴ 10
0
votes
0
replies
1.7k
views
Job: Research Assistant in the Systems Environmental Microbiology Group at DTU Biosustain
engineering Strain
4.4 years ago by info ▴ 90
1
vote
1
reply
992
views
CNV in EPIC Illumina DNA methylation
bed CNV Conumee
updated 2.7 years ago by 45k • written 4.5 years ago by • 0
4
votes
4
replies
3.0k
views
awk, count and print the number of lines following a separator then add value of header to that column
awk
updated 4.5 years ago by 12k • written 4.5 years ago by ▴ 20
1
vote
2
replies
1.8k
views
FastQC report of the metagenomic data
Metagenomics Microbiome WholeShotgunMetagenome FastQC Data-Analysis
4.5 years ago by serene.s • 0
0
votes
1
reply
1.0k
views
copy number variation and aneuploidy
aneuploidy number copy variation
updated 4.5 years ago by ★ 3.0k • written 4.5 years ago by • 0
0
votes
4
replies
1.8k
views
Getting biological replicates from SRA run NCBI
fastq AWS SRA RNAseq
20 months ago by Andres ▴ 20
0
votes
1
reply
1.5k
views
Forum: Opinions on SLAM-Seq for Differential Gene Analysis
DGE RNA-Seq htseq
updated 4.5 years ago by ★ 7.8k • written 4.5 years ago by ▴ 70
1
vote
2
replies
1.8k
views
Basic questions about SPAdes, metaSPAdes
metaspades
4.5 years ago by yingcraft • 0
0
votes
3
replies
4.9k
views
Questions on ssGSEA
RNA-seq gsva ssGSEA alignment
updated 4.5 years ago by ▴ 90 • written 4.5 years ago by ▴ 80
0
votes
1
reply
751
views
.bam .sam paired or unique aligment
aligment sam bam
updated 2.7 years ago by 45k • written 4.5 years ago by • 0
6
votes
3
replies
1.6k
views
Tool for Protein Alignment/Superimposition
protein superimposition alignment
4.5 years ago by antoniaa ▴ 30
1
vote
3
replies
1.4k
views
Cannot great a gene by gene matrix in Rstudio
gene matrix
updated 3.0 years ago by 45k • written 4.5 years ago by • 0
6
votes
10
replies
2.4k
views
what does very low estimates but a significant P value mean.
coefficients pvalue regression
updated 4.4 years ago by ★ 3.1k • written 4.5 years ago by ▴ 10
1
vote
1
reply
1.5k
views
How can I compare the similarities of two transcriptomes?
transcriptome similarity rnaseq
updated 4.5 years ago by ★ 1.1k • written 4.5 years ago by ▴ 30
4
votes
6
replies
8.7k
views
calculate ti/tv ratio in WGS data
sequencing ti/tv ratio
updated 4.5 years ago by • 0 • written 7.6 years ago by ▴ 10
0
votes
1
reply
909
views
what is the length of sliding window in trimming options how to get it
fastq fasta SRA
updated 2.7 years ago by 45k • written 4.5 years ago by ▴ 20
1
vote
1
reply
2.6k
views
RNA-seq gene list - HOMER Gene based analysis
RNA-Seq homer
updated 4.5 years ago by ▴ 370 • written 8.4 years ago by ▴ 20
3
votes
4
replies
2.0k
views
Duplicate ID error with update-name flag
Chromosome SNP position Plink unix rsid
updated 4.5 years ago by 12k • written 4.5 years ago by ▴ 20
0
votes
1
reply
1.2k
views
Generating multiple species consensus alignments for tree topology tests
bcftools alignment fasta iqtree vcf
updated 4.5 years ago by ▴ 160 • written 4.5 years ago by ▴ 40
1
vote
8
replies
2.3k
views
How to map rsIDs to KEGG variant Ids
dbsnp kegg rsid
4.5 years ago by david.f.stein ▴ 10
0
votes
1
reply
1.1k
views
blastn cut off values
blast
updated 4.5 years ago by ▴ 160 • written 4.5 years ago by ▴ 70
2
votes
1
reply
5.6k
views
vcftools and SnpSift give different values for Ts/Tv ratio
variant SNP vcf transversion transition
updated 4.1 years ago by 45k • written 10.8 years ago by ▴ 380
13
votes
6
replies
12k
views
6 follow
convert sam into paf format
genome alignment sequencing assembly SNP
updated 2.9 years ago by ▴ 30 • written 4.9 years ago by ▴ 10
0
votes
4
replies
1.5k
views
add text to a path by adding text to it with python (FTP Path NCBI)
python ncbi pandas
4.5 years ago by Debut ▴ 20
1
vote
0
replies
938
views
Job: Opportunity: Bioinformatics Software Engineer - Bioinformatics Core @ Memorial Sloan Kettering Cancer Center, New York, NY (US)
cancer_biology Python R
updated 4.4 years ago by 45k • written 4.5 years ago by ▴ 10
0
votes
1
reply
857
views
Differential Expression Analysis Using RPKM
RPKM RNA-seq DE
updated 4.5 years ago by 15k • written 4.5 years ago by • 0
1
vote
1
reply
1.1k
views
Single cell clusters annotating to same cell-type
Monocle Single-cell Seurat Pseudotime
updated 4.5 years ago by ★ 1.1k • written 4.5 years ago by ▴ 50
0
votes
2
replies
1.3k
views
Exact duplicated reads between independent replicates
ChIP NGS low-input duplicates Illumina
4.5 years ago by Miguel • 0
0
votes
1
reply
2.0k
views
Surat object UMAP - highlight cells based on Citeseq data
Seurat UMAP
updated 4.5 years ago by 3.4k • written 4.5 years ago by ▴ 40
2
votes
1
reply
1.1k
views
Obtaining all independent SNPs
SNPs permutation pruning clumping PLINK
updated 4.5 years ago by ★ 4.8k • written 4.5 years ago by ▴ 10
1
vote
2
replies
1.3k
views
Cytoscape for co-occurence network analysis
Microbiome 16S analysis Cytoscape Network
4.5 years ago by Bioinfonext ▴ 480
3
votes
2
replies
2.4k
views
Structural variants calling in a population
structural variants
updated 4.5 years ago by • 0 • written 8.5 years ago by ★ 1.0k
5
votes
4
replies
7.7k
views
Merge vcf files of structural variants
structural_variants vcf merge
updated 4.5 years ago by • 0 • written 7.3 years ago by ▴ 20
3
votes
2
replies
4.4k
views
For loop to parallel run commands
Unix bash Linux
4.5 years ago by endretoth ▴ 40
122,198 results • Page 640 of 2444
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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
Comment: ID unifiying across different datasets
Comment: snpEff: Unsupported structural variant types
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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?
Comment: Access to bulk FAST5 datasets by matt_arnold_bio • 0
Just bumping this to see if anyone knows where I can download example **bulk** files (i.e. files containing metadata allowing simulated pla…
Answer: direct RNA long-reads alignment against reference genome by GenoMax 154k
> Can I align these reads against a reference genome directly? I Yes you can with the following pre-set as noted in `minimap2` quick guid…
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