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122,008 results • Page 274 of 2441
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How to get rid of all copies of repeated lines in BLAST result text files
BLASTX Python BLAST
updated 2.5 years ago by ▴ 30 • written 2.6 years ago by ▴ 10
0
votes
1
reply
874
views
More than one proteins in one row in mass spectrometry data
proteomics mass_spectrometry
updated 2.5 years ago by 89k • written 2.5 years ago by ▴ 20
0
votes
1
reply
1.1k
views
adding transcripts ID to the REVEL score
annotation revel
2.5 years ago by Manuel ▴ 50
1
vote
3
replies
1.3k
views
Detecting heterozygous deletions in NGS sequence data
fastq vcf GATK
2.5 years ago by shpak.max ▴ 60
4
votes
2
replies
1.7k
views
SKAT TEST
pvalue SKAT SNP R VCF
updated 2.5 years ago by 23k • written 2.5 years ago by ▴ 40
1
vote
2
replies
1.4k
views
Taxonomy from blast file
blast taxonomy
updated 2.5 years ago by ▴ 150 • written 2.5 years ago by ▴ 50
6
votes
3
replies
1.6k
views
trimmomatic and STAR alignments
trimmomatic STAR RNAseq sequencing reads
updated 2.4 years ago by ▴ 140 • written 2.5 years ago by ▴ 80
10
votes
7
replies
3.2k
views
How do I use GNU parallel with two inputs?
parallel GNU
updated 2.5 years ago by ★ 4.5k • written 2.5 years ago by ▴ 10
0
votes
1
reply
932
views
TypeError: 'list' object is not callable
List dataFrame python
updated 2.5 years ago by ▴ 10 • written 2.5 years ago by ▴ 50
0
votes
1
reply
1.1k
views
VEP tool
VEP
updated 2.5 years ago by 89k • written 2.5 years ago by • 0
0
votes
0
replies
570
views
Recommendation for de novo scaffolder
Assembly Genome
2.5 years ago by atia.amin2010 • 0
2
votes
2
replies
1.1k
views
i want to replace accession number with gene name?
fasta
2.5 years ago by Neel ▴ 20
0
votes
4
replies
1.8k
views
Demultiplex droplet single-cell RNA-seq data based on sex
scRNA-seq demultiplexing HTO vireo cell hashing
updated 11 months ago by ▴ 30 • written 2.5 years ago by • 0
0
votes
0
replies
642
views
Forcefiled for methyl arsonous acid
simulation Forcefiled molecular dynamic
2.5 years ago by Peerzada ▴ 10
13
votes
17
replies
4.8k
views
6 follow
Differential Expression of Targeted RNA-Seq
rna-seq R
updated 2.5 years ago by ▴ 40 • written 7.9 years ago by ▴ 50
0
votes
1
reply
791
views
Identifying the different types of source assay data
sourceassay DNAseq ChipSeq MNase
updated 2.5 years ago by 89k • written 2.5 years ago by • 0
0
votes
1
reply
974
views
Protein search against a database and then cluster
clustering amino-acid search similarity
updated 2.5 years ago by ★ 30k • written 2.5 years ago by • 0
19
votes
14
replies
3.6k
views
7 follow
Forum: What's the general view on point & click bioinformatics for routine analyses?
ngs RNA-Seq next-gen-sequencing
2.5 years ago by Simon ▴ 40
1
vote
2
replies
1.2k
views
Extract a number after a tab as a single line
Perl Regex
updated 2.5 years ago by ▴ 60 • written 2.5 years ago by • 0
3
votes
2
replies
986
views
Error using BWA to map environmental transcriptome against a genomic reference
BWA
updated 2.4 years ago by 45k • written 2.5 years ago by ▴ 20
0
votes
0
replies
675
views
software and publicly available datasets for eQTLs?
eqtls
2.5 years ago by User 7754 ▴ 290
2
votes
6
replies
2.1k
views
Older version of SVA (Surrogate Variable Analysis) in R using Bioconductor?
Bioconductor SVA
2.5 years ago by mropri ▴ 170
0
votes
3
replies
1.7k
views
How to tell which exon does a variant located?
HGVSc HGVSp variant exon
updated 2.5 years ago by 45k • written 2.5 years ago by • 0
1
vote
4
replies
1.6k
views
How do you find two genes exclusively expressed in a given tissue / cell type?
gene-expression
updated 2.5 years ago by ★ 1.6k • written 2.5 years ago by • 0
0
votes
0
replies
1.2k
views
Illumina Infinium Human Global Screening Array manifest file
microarray Illumina Genotyping
updated 2.5 years ago by 45k • written 2.5 years ago by ▴ 30
3
votes
1
reply
1.1k
views
Can BWA align genome fasta to fasta?
BWA VCF
updated 2.5 years ago by 103k • written 2.5 years ago by • 0
10
votes
10
replies
2.7k
views
efetch problem on ARM Mac
efetch entrez-direct conda
2.5 years ago by frabomba6 ▴ 40
2
votes
4
replies
1.4k
views
Whole genome to whole exome data
whole-exome-sequencing whole-genome-sequencing
updated 2.5 years ago by 154k • written 2.5 years ago by ▴ 20
0
votes
0
replies
529
views
Best way to find co-regulated transcripts in TCGA data set
co-regulation TCGA
updated 2.5 years ago by 45k • written 2.5 years ago by ▴ 50
0
votes
0
replies
702
views
false positives in taxonomic classification reports
metagenomics kraken taxonomy kraken2
updated 2.5 years ago by 45k • written 2.5 years ago by ▴ 10
2
votes
1
reply
924
views
Change sequence ID in fastq file generated by bcftools mpileup
bcftools
updated 2.3 years ago by 45k • written 2.5 years ago by ▴ 20
46
votes
9
replies
49k
views
7 follow
Tool: Tools to merge overlapping paired-end reads
ngs Assembly fastq
updated 2.5 years ago by ▴ 70 • written 8.9 years ago by ★ 1.2k
17
votes
14
replies
33k
views
13 follow
Merge Paired-End Reads
fastq
updated 2.5 years ago by 45k • written 14.0 years ago by 11k
3
votes
4
replies
1.6k
views
How to filter bam file for only reads that span certain regions of the genome?
reference-genome bam sam bedtools
updated 2.5 years ago by 45k • written 2.5 years ago by • 0
1
vote
2
replies
1.3k
views
Advice about building a computational project to investigate porphyrin’s roles in cancer survival for a newbie in bioinformatics
machine-learning python data-mining
updated 2.5 years ago by ★ 7.7k • written 2.5 years ago by • 0
0
votes
1
reply
790
views
Phasing softwares
Phasing beagle
updated 2.5 years ago by 8.0k • written 2.5 years ago by ▴ 30
0
votes
0
replies
583
views
Does the bigwig file of a single-end chip-seq shows 2 peaks for a fragment whereas the paired-end show one peak ?
peak chip-seq bigwig single-end
updated 2.5 years ago by 45k • written 2.5 years ago by ▴ 20
0
votes
2
replies
1.3k
views
Phytochemical databases disappearing?
database
updated 2.5 years ago by • 0 • written 5.3 years ago by • 0
0
votes
1
reply
2.9k
views
Calculating fold 80 base penalty by hand
base-penalty WES Fold-80 Picard
updated 2.5 years ago by 45k • written 2.5 years ago by • 0
0
votes
2
replies
1.0k
views
How to add attributes (i.e. gene_id, transcipt_id, exon_id, etc.) annotation from .bed file onto VCF?
vcf gtf bcftools
2.5 years ago by yuuniper • 0
0
votes
0
replies
601
views
Best way to design PCR primers to differentiate fungi strains? Should I be targeting structural variants?
structural-variants PCR short-read fungi
updated 2.5 years ago by 45k • written 2.5 years ago by • 0
0
votes
1
reply
731
views
Are there newer versions of NCBI Protein Clusters?
ncbi database
updated 2.5 years ago by 154k • written 2.5 years ago by ▴ 80
5
votes
6
replies
2.2k
views
How many CPUs should I use in my SLURM job for my BLAST?
blast slurm hpc cpu
2.5 years ago by M. ▴ 40
15
votes
2
replies
1.8k
views
Pooling animal samples to a lower number of replicates vs. sequencing a subgroup of the animal
experimental-design RNA-seq RRBS
updated 2.5 years ago by 22k • written 2.5 years ago by ▴ 70
6
votes
5
replies
6.0k
views
How to force bcftools to call all variants
calling bcftools mpileup variant call
updated 2.5 years ago by 154k • written 4.5 years ago by ▴ 150
2
votes
1
reply
1.4k
views
Calculate the kinship matrix from NGS data
PCangsd kinship BEAGLE ANGSD
updated 2.5 years ago by 11k • written 2.5 years ago by ▴ 210
4
votes
4
replies
1.6k
views
Error in loading DESeq2
R DESeq2
updated 2.5 years ago by 89k • written 2.5 years ago by ▴ 60
0
votes
7
replies
1.5k
views
divide coordinates into equal number of bins
r granges
2.5 years ago by DARLOR ▴ 10
0
votes
3
replies
1.3k
views
Non-zero expression counts from deleted genes
TPM RNA-seq copy-number TCGA
updated 2.5 years ago by 4.2k • written 2.5 years ago by ▴ 90
0
votes
2
replies
1.1k
views
How to remove the contaminant reads from plants sequencing
contaminant plants genome
updated 2.5 years ago by ★ 1.8k • written 2.5 years ago by • 0
122,008 results • Page 274 of 2441
Recent Votes
Answer: DESeq2 on metagenome KO counts
Answer: DESeq2 on metagenome KO counts
Comment: GUI commercial software for 10x single cell gene expression analysis
Answer: GUI commercial software for 10x single cell gene expression analysis
Answer: GUI commercial software for 10x single cell gene expression analysis
Answer: GUI commercial software for 10x single cell gene expression analysis
C: What Does Cds And Exon Mean In A Gtf File?
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Recent Replies
Comment: DESeq2 on metagenome KO counts by ATpoint 89k
Both vst or logcpm will favor expression level (magnitude of counts) rather than differences in a hclust/heatmap. For differences you need …
Comment: DESeq2 on metagenome KO counts by ATpoint 89k
The DESeq2 developer has advised many times against DESeq2 for metagenomics. Please search for related posts over at support.bioconductor.o…
Answer: DESeq2 on metagenome KO counts by andres.firrincieli 3.9k
I wouldn’t use DESeq2 on aggregated raw counts per KO, because doing so means accepting two pretty big assumptions: 1. All genes with t…
Answer: DESeq2 on metagenome KO counts by Aleksandra ▴ 180
(I apologise for my previous reply; I wanted to be as detailed as possible) DESeq2 handles KO counts perfectly well. For a time-series des…
Comment: DESeq2 on metagenome KO counts by Aleksandra ▴ 180
I apologise for how that sounded; I wanted to be as detailed as possible.
Comment: GUI commercial software for 10x single cell gene expression analysis by Istvan Albert 103k
A comment on: "*Wonky analysis is possible even with open-source R libraries.*" True - and arguably, the risk of a wonky analysis is actua…
Comment: GUI commercial software for 10x single cell gene expression analysis by GenoMax 154k
`Trailmaker` likely only supports Parse's evercode data. <br> `BioTuring` does not appear to have published pricing. <br> `Rosalind` appear…
Answer: GUI commercial software for 10x single cell gene expression analysis by firestar ★ 1.7k
Found a few more when I asked around. I have no idea how good or bad these are. If anyone has used these or knows more about these, feel fr…
Comment: How to handle TrEMBL proteins without gene annotation in plasma proteomics? by GenoMax 154k
> I performed a standard proteomics screening workflow What database did you use to search against? Perhaps you are using an old (not so c…
Answer: FACS quality control based on size and doublet detection in scRNA-seq by ATpoint 89k
No, it's unrelated. Doublets in 10x happen if two cells get enclosed into the same GEM droplet. This has nothing to do with how flow cytome…
Answer: How to handle TrEMBL proteins without gene annotation in plasma proteomics? by Elisabeth Gasteiger ★ 2.4k
Apparently you are working with human proteins? I would strongly recommend looking only at proteins that are part of the human reference pr…
Comment: Tools to simulate Illumina short read sequences and ONT long reads with a refere by colindaven 8.0k
Wow, thats too long. How much RAM does your machine have, it is likely swapping
Comment: How to handle TrEMBL proteins without gene annotation in plasma proteomics? by Elisabeth Gasteiger ★ 2.4k
Note that UniProtKB accession numbers do not have any meaning. While most ACs starting with A0A5* are indeed unreviewed (i.e. from TrEMBL),…
Comment: DESeq2 on metagenome KO counts by young_bioinformatician ▴ 240
Thank you but sorry, your answer sounds very AI-based...
Answer: How to handle TrEMBL proteins without gene annotation in plasma proteomics? by Aleksandra ▴ 180
For basic analysis, discard anything that isn't from Swiss-Prot. Your statistics and pathway analysis should only be based on reliable, ann…
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