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Plotting Differential Induced Genes across timepoints in DESEQ2
Bioconductor DESEQ2 MA RNA-seq
updated just now by 47k • written 14 minutes ago by • 0
0
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3
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23
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Forum: What to put in my Github
Github
updated just now by 47k • written 43 minutes ago by • 0
0
votes
0
replies
7
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What criteria follow in order to choose the crystaline structure of a molecule
Molecular Docking
40 minutes ago by roybatty269 • 0
0
votes
1
reply
8
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Quantify inactivated virus particles
virus quantification offtopic
updated just now by 47k • written 47 minutes ago by • 0
2
votes
2
replies
529
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Recombination maps for cattle
SNP IMPUTE2 genome Assembly
updated 1 hour ago by • 0 • written 18 months ago by ▴ 10
0
votes
1
reply
17
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Samtools view filter by reference sequence
samtools
updated 1 hour ago by 135k • written 1 hour ago by • 0
0
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0
replies
19
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How exactly does diffBind count reads?
atacseq diffbind
2 hours ago by iamjli ▴ 10
1
vote
8
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274
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Pacbio SRA data format error
Pacbio SRA bax2bam isoseq3
updated 2 hours ago by 99k • written 6 weeks ago by • 0
580
votes
155
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64k
views
89 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
handbook tutorial training News
updated 2 days ago by 10 • written 4.4 years ago by 87k
0
votes
0
replies
15
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The effect of heterozygosity on genome alignment
heterozigosity alignment bwa sequence
2 hours ago by Iseez • 0
1
vote
1
reply
95
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vcftools intersect vs bedtools intersect
bedtools vcf vcftools
updated 3 hours ago by 32k • written 21 hours ago by • 0
0
votes
2
replies
40
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Segmentation fault (core dumped) error in MUSCLE
NGS alignment fastq linux sequence
1 hour ago by christopherjamessteel1990 • 0
0
votes
1
reply
41
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Genome sequencing data analysis and assembly L.lactis subsp.lactis strain Lac3
well
updated 3 hours ago by ★ 10k • written 5 hours ago by • 0
0
votes
1
reply
60
views
Is it bad practice to change threshold for interaction probability?
STRING Cytoscape
updated 4 hours ago by 5.8k • written 1 day ago by ▴ 10
2
votes
2
replies
43
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bedops wig2bed 'Row begins with a tab or space' error
wig2bed bedops convert2bed
updated 3 hours ago by 32k • written 4 hours ago by • 0
0
votes
0
replies
29
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correlation analysis of a single variable versus multiple variables
correlation r RNA-Seq
updated 5 hours ago by 99k • written 5 hours ago by • 0
0
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0
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26
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Demultiplexing Samples With Contaminated Hashtag
scRNAseq seurat demultiplexing
5 hours ago by fouerghi20 ▴ 30
0
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0
replies
25
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News: Noncoding RNA Conference: upcoming abstract deadline
ncRNA conference RNA noncoding
5 hours ago by rory.johnson ▴ 20
0
votes
2
replies
81
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Variant calling from comparison of assembled genomes where there is only one read depth.
variant
updated 5 hours ago by 9.7k • written 10 hours ago by ▴ 120
1
vote
0
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31
views
Holistic enzyme activity determination with computation
protein enzymes bioinformatics proteomics
6 hours ago by birbronald9 ▴ 10
0
votes
4
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83
views
transcription factor activation order
transcription
5 hours ago by kenny • 0
0
votes
0
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21
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JoinMap4 makes a new map every time
joinmap linkage_mapping genetic_map SNP
6 hours ago by Beetle Editor • 0
0
votes
0
replies
25
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How to get all microRNA target genes?
miRNA multimir microRNA targetgenes tarbase
7 hours ago by Katarina • 0
0
votes
1
reply
50
views
LDSC -Genetic correlation, some results all have NA valuies
correlation ldsc genetic gwas
updated 7 hours ago by ★ 3.4k • written 10 hours ago by • 0
0
votes
1
reply
48
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Can Meta-GWAS summary statistic results be used for Meta-GWAS (For example, METAL)?
METAL input Meta-analysis Meta-GWAS
updated 7 hours ago by ★ 3.4k • written 12 hours ago by • 0
4
votes
5
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182
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Batch effect correction of 2 studies with different covariates
batch-effect R RNA-seq
4 hours ago by Geo ▴ 20
0
votes
1
reply
59
views
How to get GO terms to specific to perticular biological process
GO Enrichment RNA-seq
updated 7 hours ago by ▴ 110 • written 10 hours ago by • 0
1
vote
1
reply
41
views
MemoryError w/ matrix | Smith-Waterman Algorithm Python
Matrix Smith-Waterman Python Memory Memory-Error
updated 7 hours ago by 87k • written 8 hours ago by ▴ 10
0
votes
0
replies
40
views
Job: Informatician / Data Analyst | University of Glasgow
job data-analyst
8 hours ago by dariober 12k
1
vote
3
replies
158
views
IndexError: list assignment index out of range | Needleman-Wunsch Algorithm - Python
List Needleman-Wunsch Python DynamicProgramming
updated 8 hours ago by 87k • written 3 days ago by ▴ 10
1
vote
0
replies
35
views
Violin Plot for Single-cell data, gene expression in different timepoints
violin-plot gene-expression R single-cell
updated 8 hours ago by 99k • written 8 hours ago by ▴ 10
1
vote
2
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101
views
Pooling normal data in Mutect2
mutect2 pooling normal samples panelofnormals
1 hour ago by Michelle • 0
0
votes
0
replies
32
views
Convert GFF3 to splice junction BED file, for filtering variants multi-sample (RNA-seq) VCF
rna splice-junction vcf
9 hours ago by William ★ 4.8k
2
votes
3
replies
127
views
How to extract all columns of CSQ using split-vep plugin of bcftools?
plugin samtools bcftools vcf split-vep
updated 9 hours ago by ▴ 60 • written 1 day ago by ★ 1.4k
0
votes
0
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38
views
integration of single cell RNA-seq and bulk RNA-seq data
RNA-seq
9 hours ago by ramyak1912 • 0
1
vote
4
replies
101
views
how to extract REF and ALT DNA string around SNV
SNV motif
9 hours ago by shangguandong1996 ▴ 10
0
votes
0
replies
35
views
GEMINI ISSUE
BIOINFORMATICS GEMINI
updated 9 hours ago by 99k • written 10 hours ago by • 0
2
votes
0
replies
60
views
Forum: Bioinformatics startup market analysis
startup
10 hours ago by gtechbio ▴ 20
0
votes
0
replies
27
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Minimum enrichment score to take for analysis
Sequencing Rna-Seq
10 hours ago by ashwing.kofficial • 0
0
votes
4
replies
84
views
How to Estimate total variance in, and between RNA-seq datasets?
batch variance correction
7 hours ago by Gabriel ▴ 90
0
votes
1
reply
48
views
Detection of bacterial SNP using regular PCR primers
detection PCR SNP
updated 10 hours ago by ▴ 60 • written 11 hours ago by ▴ 50
1
vote
3
replies
557
views
Can't change coefficient of dds object: error 'coef' should specify same coefficient as in results 'res'
DESeq2 RNA-seq
updated 3 hours ago by 47k • written 14 hours ago by ▴ 30
0
votes
2
replies
131
views
How can I revert back the Ensembl vep annotated positions to vcf positions?
ensembl VEP VCF
updated 11 hours ago by 47k • written 2 days ago by ★ 1.4k
0
votes
0
replies
32
views
Negative branch length when using clustalw through Python and unable to see bootstrap values
clustalw Phylogeny bootstrap Python tree
13 hours ago by minifoog • 0
1
vote
3
replies
132
views
About combining the forward and reverse sequence
16srRNA geneious
updated 10 hours ago by 99k • written 2 days ago by • 0
1
vote
2
replies
121
views
cannot import name 'gcd' from 'fractions'
ubuntu Linux python multiqc
3 hours ago by h.gaikani • 0
66
votes
40
replies
21k
views
22 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
rna-seq bioconductor fpkm Forum Tutorial
updated 15 hours ago by • 0 • written 7.5 years ago by ★ 7.3k
0
votes
0
replies
82
views
<*> meaning in Vcf Output From Mpileup
mpileup missing deletion vcf
17 hours ago by breezin • 0
4
votes
6
replies
3.5k
views
Fastqc shows over-represented sequence with no sequence given?
sequencing
updated 20 hours ago by • 0 • written 5.8 years ago by ▴ 50
1
vote
3
replies
162
views
how remove large gene ontology terms from gprofiler2 output
gprofiler2 GO DEseq RNA-seq
updated 6 hours ago by 9.2k • written 1 day ago by • 0
90,370 results • Page 1 of 1808
Recent Votes
Comment: Meaning of BWA-MEM MAPQ values
A: Detecting highly variable genes within replicates
A: Detecting highly variable genes within replicates
Answer: Pooling normal data in Mutect2
Answer: How are BWA/bowtie/etc indices built for multiple fasta entries?
Answer: How are BWA/bowtie/etc indices built for multiple fasta entries?
Answer: Pacbio SRA data format error
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Recent Replies
Comment: Finding how many times a nucleotide appear in the same position by Pierre Lindenbaum 135k
cross posted: https://stackoverflow.com/questions/67060118/
Comment: What to put in my Github by GenoMax 99k
Since this is an open-ended question I am changing it to `Forum`. > I am not allowed to release my scripts or data Unless you are doing s…
Answer: What to put in my Github by jared.andrews07 9.2k
Yes, I think analyzing publicly available data is perfectly fine. Trying to reproduce their findings (or find something they perhaps missed…
Comment: Recombination maps for cattle by Azwan • 0
Hi did you found it?
Comment: How can I create an Illumina report in Linux using IDAT files? by freeseek ▴ 120
You can look at the full content of a GTC file with the following command: ``` bcftools +gtc2vcf -v <file.gtc> ```
Answer: Samtools view filter by reference sequence by Pierre Lindenbaum 135k
get the complement BED use `bedtools complement` and the scan the bam using samtools view -L complement.bed
Comment: How can I create an Illumina report in Linux using IDAT files? by freeseek ▴ 120
After you have converted your IDATs to GTCs using Illumina's iaap-cli command, the following command will produce a GenomeStudio-like table…
Comment: How are BWA/bowtie/etc indices built for multiple fasta entries? by maxrwjones898 • 0
Interesting stuff! I'm new to informatics but I'm very much enjoying learning the quirks of these bits of software... not a fan of launchin…
Comment: Segmentation fault (core dumped) error in MUSCLE by christopherjamessteel1990 • 0
Thank you so much!
Comment: Pooling normal data in Mutect2 by Michelle • 0
Thank you!
Comment: How are BWA/bowtie/etc indices built for multiple fasta entries? by Istvan Albert 87k
that's how I understood it worked, from a forum discussion on Sourceforge I believe, where the developer Heng Li talked mentioned some int…
Comment: How are BWA/bowtie/etc indices built for multiple fasta entries? by maxrwjones898 • 0
Oooh thank you for your answer - it answers my question (i.e. I can use BWA with very large and very small reference sequences, because the…
Comment: Pacbio SRA data format error by GenoMax 99k
Thank you https://www.biostars.org/u/71b2b378/ ! Only thing I would suggest is people should create a new environment for this version inst…
Answer: Pacbio SRA data format error by papodek ▴ 10
As [already said][1] by [foeckingmf][2] it seems to be a bug. I had the same problem and solved it downgrading bax2bam from version 0.0.11…
Answer: vcftools intersect vs bedtools intersect by Alex Reynolds 32k
bedops --element-of 1 <(gunzip -c merged.vcf.gz | vcf2bed -) <(sort-bed panel.bed) > subset.bed
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