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121,795 results • Page 591 of 2436
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1
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0
replies
787
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Find most similar peptide and calculate distance?
align distance sequence peptide
4.0 years ago by wormball ▴ 10
0
votes
0
replies
850
views
Herald: The Biostar Herald for Tuesday, August 17, 2021
herald
4.0 years ago by Biostar 3.6k
3
votes
3
replies
1.3k
views
Whole exome seuqencing capture sequence
Exome Sequencing Whole
updated 4.0 years ago by 4.1k • written 4.0 years ago by ▴ 60
0
votes
3
replies
2.1k
views
Issue reading fasta file with Biopython
python
4.0 years ago by Rox ★ 1.5k
0
votes
2
replies
2.9k
views
How to get data from GEO by using getGEO function ?
RNA-Seq R
updated 4.0 years ago by • 0 • written 5.4 years ago by • 0
3
votes
1
reply
2.3k
views
Interpretation of .gfa
flye bandage assembly
4.0 years ago by Rox ★ 1.5k
0
votes
0
replies
566
views
Mapping quality and XS score
igv
4.0 years ago by jennyp0706 ▴ 10
0
votes
5
replies
2.3k
views
Trimmomatic 0.39 Permission denied accessing fastq.gz
RNA-seq trimmomatic
4.0 years ago by e.wing • 0
4
votes
6
replies
5.6k
views
Ion Torrent BAM and FASTQ
NGS TorrentBaseCaller FASTQ BAM IonExporter
updated 4.0 years ago by 11k • written 4.0 years ago by • 0
0
votes
1
reply
936
views
Using protein domains for annotation validation
Interpro annotation domain InterproScan
updated 4.0 years ago by 27k • written 4.0 years ago by ★ 1.5k
4
votes
2
replies
1.6k
views
Ubuntu on Windows 10 - using Command line
Commandline Linux Git Ubuntu
4.0 years ago by WUSCHEL ▴ 860
1
vote
1
reply
887
views
extract entire header from BED file to FASTA
bedtools getfasta
updated 4.0 years ago by ★ 1.5k • written 4.0 years ago by ▴ 20
3
votes
3
replies
1.2k
views
Develop a new RNA Seq pipeline
Rna-seq pipeline
updated 3.1 years ago by ▴ 360 • written 4.0 years ago by • 0
0
votes
1
reply
1.0k
views
Extracting variations in the gene regions and from 100 bp of gene boundary from multiple VCF files
VCF Variations
updated 4.0 years ago by ★ 1.1k • written 4.0 years ago by ▴ 100
0
votes
0
replies
549
views
Codeml giving different chi2 values when reducing the number of sequences
PAML CODEML
4.0 years ago by Amay ▴ 10
0
votes
0
replies
641
views
VcfSampleCompare - empty output with warnings
VcfSampleCompare empty warnings
4.0 years ago by Michal Nevo ▴ 140
0
votes
0
replies
708
views
PCA on pooled and single individuals
PCA analysis component pooled principal structure samples population
4.0 years ago by javiergandasegui • 0
0
votes
0
replies
628
views
KAAS: Limiting The Genes Associated With a Pathway to a Certain Species
KEGG KAAS pathway metabolic
4.0 years ago by adhamzul ▴ 20
4
votes
5
replies
3.5k
views
6 follow
TopHat error: IOError [errno 2] No such file or directory: '-o'
RNA-Seq rna-seq alignment software error
updated 6.4 years ago by ★ 4.2k • written 6.4 years ago by • 0
0
votes
0
replies
652
views
Extract peptide information from proteomics data
proteomics peptide
4.0 years ago by Gene_MMP8 ▴ 240
0
votes
0
replies
434
views
linking RNA-seq data with GWAS study
ngs
4.0 years ago by hafiz.talhamalik ▴ 350
11
votes
7
replies
15k
views
How to include/keep only the samples in a list in VCF.gz file?
vcf samples bcftools
updated 2.7 years ago by 166k • written 7.1 years ago by ▴ 210
0
votes
0
replies
960
views
What is a good Standardized Beta/standardized regression coefficient in a genetics study?
regression genetics genomics
updated 2.4 years ago by 45k • written 4.0 years ago by ▴ 210
0
votes
0
replies
911
views
Job: Postdoc at Stanford working on mobile health device data from My Heart Counts
ai science device mhealth data
4.0 years ago by hershman ▴ 40
2
votes
2
replies
1.0k
views
Download nucleotide sequence with locus_tag
SEQUENCE LOCUS_TAG NUCLEOTIDE NCBI
4.0 years ago by DJ_MB • 0
6
votes
13
replies
8.3k
views
9 follow
VCF file phasing by SHAPEIT
vcf phasing whole genome shapiet
updated 4.0 years ago by 2.9k • written 6.7 years ago by ★ 1.9k
0
votes
1
reply
1.2k
views
Differential Gene Expression after batch correction with DESC?
DESC scRNAseq batch-effect
updated 12 months ago by 45k • written 4.0 years ago by ▴ 80
2
votes
3
replies
1.9k
views
how htseq-count counts unstranded RNA-seq data
htseq-count RNA-seq stranded
updated 4.0 years ago by 15k • written 4.0 years ago by ▴ 40
0
votes
0
replies
592
views
Impute expression from bulk ATAC data
RNA Imputation ATAC
4.0 years ago by kvshamsudheen ▴ 120
1
vote
1
reply
979
views
how to apply DE-kupl in my data for differential expression ?
DE-kupl DE
updated 4.0 years ago by 89k • written 4.0 years ago by ▴ 30
5
votes
7
replies
4.4k
views
Signac CallPeaks from multiple fragment files
Seurat Macs2 Signac
3.9 years ago by LacquerHed ▴ 30
0
votes
0
replies
625
views
PDBePISA calls monomers heteromers, how can one programmatically correct this downstream
PDBe quaternary PISA structure
4.0 years ago by plberry ▴ 30
1
vote
4
replies
1.7k
views
Demultiplexing with Linux
Demultiplexing Linux
updated 4.0 years ago by 21k • written 4.0 years ago by • 0
1
vote
1
reply
2.0k
views
makeblastdb Bus error
bus-error blast
updated 14 months ago by 45k • written 4.0 years ago by ▴ 10
3
votes
10
replies
5.0k
views
6 follow
How do I match my transcript ID's from NCBI to the corresponding gene ID's to enable tximport into R?
Salmon tximport RNA-Seq R
updated 3.1 years ago by 153k • written 4.0 years ago by • 0
0
votes
2
replies
2.8k
views
How to change the track background color of IGV
IGV
4.0 years ago by changxu.fan ▴ 80
0
votes
7
replies
1.8k
views
sortsam. picard
picard
updated 4.0 years ago by 45k • written 4.0 years ago by • 0
0
votes
0
replies
642
views
Pathway enrichment for draft gene names
pathway-enrichment
updated 2.2 years ago by 45k • written 4.0 years ago by ▴ 30
1
vote
2
replies
1.6k
views
HTSeq-count TruSeq RNA Exome Lib Prep
HTseq strandness TruSeqRNAExome nofeatures
4.0 years ago by tdfyoder ▴ 40
0
votes
0
replies
1.6k
views
Job: Science Infrastructure Manager
management infrastructure project Science
4.0 years ago by EMBL Recruitment ▴ 30
1
vote
2
replies
1.1k
views
Accuracy Assembly's contigs
NGS Assembly whole genome Velvet
4.0 years ago by askari.arezou94 ▴ 30
0
votes
0
replies
679
views
Non-symmetric MA-plot (DESeq2)
MA-plot DESeq2
4.0 years ago by mdidish • 0
4
votes
7
replies
2.8k
views
Inferring CNVs from BAM files with SAMTools depth
samtools bam wes wgs cnv
updated 4.0 years ago by ★ 3.0k • written 4.0 years ago by ▴ 30
1
vote
1
reply
960
views
Base recalibration -Java run time error and no sequence dictionary
base GATK NGS recalibration
updated 4.0 years ago by ▴ 840 • written 4.0 years ago by ▴ 70
0
votes
1
reply
881
views
EQTL analysis
sQTL eQTL and
updated 4.0 years ago by ★ 3.3k • written 4.0 years ago by ▴ 50
0
votes
1
reply
838
views
Manhattan Plot in R with 100 non-numeric contigs and chromosomes
contigs chromosomes R Manhattan non-numeric
updated 4.0 years ago by 12k • written 4.0 years ago by ▴ 140
1
vote
2
replies
3.2k
views
Filter on Allele Balance using BCFTools
bcftools allele filter balance
updated 3.8 years ago by ★ 9.6k • written 4.0 years ago by ▴ 50
6
votes
9
replies
3.0k
views
Identification of transcription factors from a list of DEGs
DEGs TFs
4.0 years ago by navamikrishna99 ▴ 10
1
vote
0
replies
1.1k
views
Job: Bioinformatician — Biological data and network analysis
network-analysis Biological-data
updated 2.7 years ago by 45k • written 4.0 years ago by ▴ 30
0
votes
1
reply
934
views
how to find interference residue
protein
updated 4.0 years ago by ★ 29k • written 4.0 years ago by ▴ 920
121,795 results • Page 591 of 2436
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Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
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A: fgsea: What does fgseaMultilevel argument sampleSize mean/when to change it?
Custom Selection of GO Terms or Pathways in EnrichR Output
A: What is the difference between NZ_ and NC_ identifiers at NCBI?
Answer: Add NES value to GSEA plot
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Recent Replies
Answer: RTG (Real Time Genomics) docker image - Problem dealing with different VCFs by Jeremy Leipzig 23k
which columns are giving you trouble? is the problem that you have two samples in dragen (tumor/normal) and only one sample in the hg008?
Comment: How to obtain a refFlat file for the Rat by AIMAR ▴ 70
I've try the mentioned methods but nothing work that's why I've asked again If I can find a new solution. Thanks !
Answer: How to obtain a refFlat file for the Rat by GenoMax 153k
Please don't ask the same question again in a new thread. This was answered a few weeks back: https://www.biostars.org/p/9613666/#9613671 …
Answer: Is a direct comparison of the number of up- and down-regulated genes meaningful? by benformatics 4.1k
Usually it is not very useful. The only situation where it makes sense to use is where you do a gradient treatment (e.g. 0M, 5M, 50M, et…
Answer: Is a direct comparison of the number of up- and down-regulated genes meaningful? by ATpoint 89k
No, don't rely on numbers. This can and is strongly influences by the sample size and noise, and by this power. Even at same sample size it…
Comment: Pseudobulk analysis using AggregateExpression() by adhisadi • 0
Hi, Did you figure this out? In my data some gene expressed in very low number of cells (less than 1% of total cells) appear as differentia…
Answer: Is a direct comparison of the number of up- and down-regulated genes meaningful? by kalavattam ▴ 370
*“Within a single experiment”* is O.K. with caveats. Comparing the number up versus the number down inside a single, well-designed experime…
Comment: Is a direct comparison of the number of up- and down-regulated genes meaningful? by GenoMax 153k
What do you mean by "directly compare"? Actual number of genes in the two groups don't have a special meaning. They will change based on …
Comment: RNA seq batch correction with technical replicates by Li • 0
Samples for condition B were made into two different sets of libraries for batch 1 and 2. The person who did the experiment has left, so I …
Comment: CUT&Tag signal normalization for generating bigWig files by ATpoint 89k
I would ignore the IgGs and only use it during peak calling. For the IP samples I would do https://www.biostars.org/p/413626/#414440
Comment: CUT&Tag signal normalization for generating bigWig files by RD ▴ 20
CUT&Tag shares protocol similarities with ATAC-seq, so I'd recommend using RPGC normalization via DeepTools. You might also consider testin…
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by swbarnes2 15k
You generally can't correct for replicates in such a tiny experiment like this, so I'd drop that element. But yes, if you want to do an …
Comment: BLAST Database error: Database memory map file error by goubert.clement ▴ 30
This is the way
Answer: How to detect divergent domains in AlphaFold models (CDD/InterProscan not workin by Mensur Dlakic ★ 29k
There isn't much beyond InterPro and CDD that would automatically detect divergent domains, as those databases already include almost all o…
Comment: Web Scraping and Text Analysis in R (March 21st - April 11th, 2025) Course by Ram 45k
That's a good approach. Personally, I copy-paste text and then extract info from that text file - you can see how prohibitive it can be to …
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