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172 results • Page 1 of 4
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40
votes
10
replies
42k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma sva Combat batch-effect
updated 3 days ago by ▴ 40 • written 6.7 years ago by ★ 1.3k
38
votes
24
replies
1.9k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq STAR NGS Illumina
updated 2 days ago by 19k • written 5 days ago by ▴ 580
28
votes
28
replies
34k
views
11 follow
Split Fastq Files Into Chunks Of 1M Reads
split fastq
updated 6 hours ago by • 0 • written 12.8 years ago by ★ 1.7k
19
votes
11
replies
14k
views
10 follow
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
utr
updated 6 days ago by ★ 3.8k • written 10.8 years ago by ▴ 920
10
votes
6
replies
9.9k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly rna-seq alignment
updated 6 days ago by ★ 5.1k • written 6.0 years ago by ▴ 510
9
votes
10
replies
409
views
6 follow
Bacterial plasmid analysis
bacteria plasmid wgs hybridassembly sequencing
updated 8 hours ago by ▴ 20 • written 1 day ago by • 0
8
votes
16
replies
936
views
How to convert plink files to Hapmap Format
GWAS Plink
updated 6 days ago by ★ 2.4k • written 8 weeks ago by • 0
5
votes
4
replies
337
views
Forum: Ideal PC configurations and operating system for bioinformatics laboratory
PC
10 hours ago by Estevão • 0
5
votes
3
replies
251
views
6 follow
Integrate transcriptomic data and proteomics data.
OMICS
updated 2 days ago by ★ 1.2k • written 2 days ago by • 0
5
votes
5
replies
188
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA DADA2 metabarcoding
updated 10 hours ago by ▴ 30 • written 13 hours ago by ▴ 150
5
votes
16
replies
687
views
How many reads for WGS Sequencing?
WGS Bacterial-Genomics
3 days ago by Ruqaiya • 0
5
votes
6
replies
487
views
Programmatically retrieving positions of protein active site residues
Uniprot PDB Proteins
updated 2 days ago by ▴ 760 • written 3 days ago by ▴ 40
4
votes
6
replies
3.8k
views
Taking the difference of two VCFs (or removing singletons)
genome sequencing singleton SNP filter
updated 2 days ago by ▴ 20 • written 9.6 years ago by ▴ 40
4
votes
4
replies
437
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 5 days ago by ★ 1.7k • written 7 days ago by ★ 3.9k
4
votes
7
replies
571
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity scVelo scRNA-seq splicing
3 days ago by e.r.zakiev ▴ 210
4
votes
2
replies
294
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma voom R
3 days ago by pairedttest ▴ 10
4
votes
0
replies
128
views
Herald: The Biostar Herald for Monday, April 29, 2024
herald
3 days ago by Biostar 2.7k
4
votes
8
replies
642
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs BED eqtl bedtools
updated 5 days ago by 35k • written 6 days ago by ▴ 10
4
votes
2
replies
394
views
Missing protein (VEGF-A) in String db
VGFA stringdb
updated 6 days ago by • 0 • written 12 weeks ago by ▴ 20
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference 38build impute imputation
3 days ago by anna ▴ 20
4
votes
5
replies
282
views
High Malat-1 expression in single cell data
cell analysis single
updated 3 days ago by ★ 5.9k • written 3 days ago by ▴ 10
4
votes
7
replies
680
views
7 follow
Heatmap and rna-seq
RNA-Seq Heatmap
updated 5 days ago by ★ 5.9k • written 9 days ago by ▴ 10
4
votes
3
replies
359
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc conda nextflow
updated 5 days ago by 3.2k • written 6 days ago by ▴ 40
3
votes
0
replies
199
views
News: Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy Generative-AI scRNA Machine-Learning
updated 6 days ago by 43k • written 6 days ago by ▴ 60
3
votes
2
replies
328
views
what is the purpose of indexing the reference genome (Kallisto)
indexing Kallisto
updated 6 days ago by ★ 5.9k • written 6 days ago by ▴ 10
3
votes
8
replies
6.5k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk genomicsdbimport
updated 5 hours ago by • 0 • written 5.1 years ago by 11k
3
votes
7
replies
315
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc cutadapt illumina tile paired-end
3 days ago by salias • 0
3
votes
3
replies
309
views
Is it possible to bulk download files from GEO repository?
RNA-seq Galaxy Tanscriptomics
updated 3 days ago by ▴ 580 • written 3 days ago by ▴ 750
3
votes
2
replies
288
views
ChIP-seq datasets: input samples omitted?
ChIP-seq Normalization NGS
updated 3 days ago by 19k • written 6 days ago by ▴ 40
3
votes
3
replies
300
views
genome assembly records not present in assembly_summary.txt
ncbi bacteria assembly
updated 6 days ago by 142k • written 6 days ago by ▴ 10
3
votes
6
replies
2.0k
views
7 follow
DNA methylation preprocessing
SWAN DNA methylation Funnorm
updated 6 days ago by 43k • written 2.4 years ago by ▴ 10
3
votes
2
replies
362
views
Extract protein sequence
fasta alignment blast
2 days ago by anna ▴ 20
2
votes
4
replies
273
views
from row count to tpm
tpm row-count normalization
updated 2 days ago by 43k • written 10 days ago by ▴ 20
2
votes
2
replies
183
views
MA plot of shrunken fold change
MA-plot Deseq2
updated 2 days ago by 82k • written 2 days ago by • 0
2
votes
11
replies
891
views
Questions about a bug when transferring cram file to bam file
sequence samtools bcftools
updated 3 days ago by ★ 1.2k • written 15 days ago by • 0
2
votes
5
replies
158
views
How to access TCGA samples that were treated with a specific drug?
TCGA RNA-seq
updated 36 minutes ago by 142k • written 7 hours ago by ▴ 40
2
votes
4
replies
2.6k
views
When to use .vcf or .gvcf files from GATK HaplotypeCaller?
indel gatk calling snp variant
updated 3 days ago by 9.7k • written 24 months ago by ▴ 120
2
votes
5
replies
926
views
Retrieval of Active site information programmatically
Catalytic Python Active PDB site Site
updated 3 days ago by ★ 2.0k • written 2.0 years ago by • 0
2
votes
5
replies
345
views
Figures are disappeared from html report of SnpEff
HTML SnpEff
3 days ago by analyst ▴ 30
2
votes
5
replies
337
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq assembly transcriptome contamination
6 days ago by Lada ▴ 30
2
votes
7
replies
1.3k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq Salmon Isoseq
updated 3 days ago by ★ 7.1k • written 8 months ago by ▴ 10
2
votes
2
replies
245
views
p-value in CIBERSORT
CIBERSORT p-value
1 day ago by michelafrancesconi9 ▴ 20
2
votes
2
replies
193
views
PDB related issue
rcsb pdb
updated 4 days ago by ▴ 580 • written 4 days ago by • 0
2
votes
3
replies
349
views
How to establish haplotype-specific gene expression levels
RNA-seq Haplotype
updated 6 days ago by ★ 5.9k • written 23 days ago by ▴ 60
2
votes
5
replies
450
views
Fetch table from clinvar database according to a list of rsid
python clinvar perl
4 days ago by ashaneev07 ▴ 20
1
vote
7
replies
482
views
gvcf joint calling
WES GATK VCF gVCF
4 days ago by zihanss • 0
1
vote
2
replies
212
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana gtf reference-genome
updated 2 days ago by 43k • written 2 days ago by • 0
1
vote
2
replies
333
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign cell-markers
5 days ago by Francesco ▴ 10
1
vote
1
reply
205
views
Polishing genome assembly
polishing Nanopore PacBio
updated 2 days ago by 54k • written 3 days ago by • 0
1
vote
0
replies
157
views
Simulation of label-free bottom-up proteomics expression dataset
label-free bottom-up lc-ms proteomics
6 days ago by KABILAN ▴ 70
172 results • Page 1 of 4
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Answer: Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
How to convert plink data from 38th assembly to 37
How to convert plink data from 38th assembly to 37
Comment: How to access TCGA samples that were treated with a specific drug?
Comment: Normalize scRNAseq data to housekeeping genes to compare several datasets
Comment: Converting CRAM to FastQ
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Recent Replies
Comment: How to access TCGA samples that were treated with a specific drug? by GenoMax 142k
It is possible that these drugs may not have been directly used in TCGA. Authors could have looked for mutations known to be acted on by th…
Comment: Does comparing two different groups to a common third group introduce bias in th by Qroid ▴ 40
Are you thinking about a specific scenario? If so, can you provide more info? I think the basic answer is that, yes, your choice of group C…
Answer: Bedtools merge minimum overlap? by harold.smith.tarheel ★ 4.9k
Bedtools [intersect][1] allows you to specify the fraction of overlap between two BED (or BAM) files using the F/f/r flags. You could split…
Comment: How to access TCGA samples that were treated with a specific drug? by Qroid ▴ 40
Sorry, I should have been more specific. By "that list" I mean what's populated in the Therapeutic Agents tab when no filters are applied. …
Comment: Bedtools merge minimum overlap? by bk11 ★ 2.4k
Not sure if you wanting to do like this- cat your_input.bed chr1 100 200 region1 + chr1 180 300 regi…
Comment: Extract gRNA sequence using cutadapt by GenoMax 142k
If you know what the boundaries of your construct look like then trim the left-end of the read using the tag on that end (`ktrim=l`). Then …
Comment: Extract gRNA sequence using cutadapt by gernophil ▴ 80
> Not every read in your data is going to match a guide. That is also true for sure. Let me clarify what I mean. For every read you should…
Answer: VG : No reference-sense paths available in the graph; falling back to generic pa by anovak ▴ 120
If your GFA has paths in it that are P lines with names that don't include a sample name, contig name, and separators, then those are what …
Comment: Extract gRNA sequence using cutadapt by GenoMax 142k
> if you look at a fastq file you should be able to tell for every read definitely, if it has a perfect match for a guide in it and what gu…
Answer: DiffBind: no peaks in DBA by jared.andrews07 ★ 16k
Because `dba.analyze` is not meant to be run directly on a peaks file. Have you read the documentation? In addition, a ChIP-seq experiment…
Comment: Converting CRAM to FastQ by Maverick ▴ 10
Thank you so much! Will look it up right away.
Comment: Extract gRNA sequence using cutadapt by gernophil ▴ 80
> I don't think every guide is supposed to show up in these experiments as far as I have seen. You will get some guides with 0 counts as yo…
Comment: Converting CRAM to FastQ by GenoMax 142k
Use `samtools view ` for this conversion. See discussion in https://www.biostars.org/p/9592860/ Specifically @jkbonfield's comment here --…
Comment: How to access TCGA samples that were treated with a specific drug? by GenoMax 142k
No that was only from Breast cancer. You could try selecting all data and see if you are able to see all treatments in the set. No idea a…
Comment: Extract gRNA sequence using cutadapt by GenoMax 142k
I don't think every guide is supposed to show up in these experiments as far as I have seen. You will get some guides with 0 counts as you …
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