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526 results • Page 2 of 11
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0
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5
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378
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Parsing fasta file by coordinates
linux fasta
updated 28 days ago by 141k • written 4 weeks ago by ▴ 120
0
votes
5
replies
488
views
How to assure that sequence consensus is genuine?
genome
19 days ago by marongiu.luigi ▴ 710
2
votes
5
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683
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 5 days ago by ▴ 740 • written 6 days ago by ★ 2.4k
0
votes
5
replies
283
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative ncbi asembly refseq
updated 21 hours ago by 141k • written 1 day ago by ▴ 90
0
votes
5
replies
285
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap alignment minimap2 GRCh38 assembly
1 day ago by njornet ▴ 20
0
votes
5
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1.2k
views
RNAseq differential gene expression analysis yield results which come from digestive content
differential-gene-expression RNA-Seq
updated 16 days ago by 43k • written 6.4 years ago by ▴ 90
0
votes
5
replies
401
views
Used featureCounts to generate a count matrix for sc RNA-seq and it has all 0s.
scRNA-seq
updated 15 days ago by 141k • written 16 days ago by • 0
0
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5
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1.8k
views
Demultiplexing multiple amplicons from one fastq based on primer sequence
demultiplexing illumina
updated 17 days ago by 3.2k • written 3.4 years ago by • 0
0
votes
5
replies
2.0k
views
Batch effect correction & normalization after training/test split for gene expression data
RNA-seq batch-effect normalization
updated 9 days ago by 43k • written 20 months ago by ▴ 60
0
votes
5
replies
289
views
How to compare bulk RNA seq data demultiplexed in different ways?
RNA-seq
updated 21 days ago by 43k • written 24 days ago by ▴ 150
3
votes
5
replies
408
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity scVelo scRNA-seq splicing
updated 22 days ago by 141k • written 23 days ago by ▴ 200
0
votes
5
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1.6k
views
what does mean this error ? "(ERR): hisat2-align exited with value 1" in mapping long noncoding RNAs
long-non-coding-RNA lncRNA
updated 20 days ago by 43k • written 2.6 years ago by • 0
0
votes
5
replies
529
views
seg fault, core dumped with manta 1.6.0
manta gdb
updated 17 days ago by 43k • written 21 days ago by • 0
0
votes
5
replies
334
views
Incongruencies in GT assignment by Freebayes
depth freebayes heterozygous genotype
20 days ago by virginia.baraja • 0
5
votes
5
replies
7.2k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq bulk-RNASeq RNA-Seq single-cell
updated 15 days ago by • 0 • written 3.8 years ago by ★ 1.8k
0
votes
5
replies
419
views
Error running local blastn in R using system2
blastn NCBI R
27 days ago by Harrison • 0
0
votes
5
replies
5.9k
views
Calculate Radius of Gyration [python 3]
biopython PDB Radius of Gyration python protein
updated 5 days ago by • 0 • written 6.5 years ago by ▴ 30
0
votes
4
replies
316
views
Questions about transfering wgs file to reference genome file
fasta cram genome
14 days ago by me • 0
0
votes
4
replies
337
views
Compute bootstrap values on consensus tree
phylogeny tree raxml
10 days ago by pablo ▴ 300
2
votes
4
replies
395
views
Per Base Sequence Content - continuous raise of G%
fastqc
updated 15 days ago by 141k • written 16 days ago by • 0
1
vote
4
replies
2.4k
views
Batch effect control in GWAS data.
Batch-effect omniexpress GWAS GSA
updated 8 days ago by 43k • written 4.8 years ago by ▴ 10
0
votes
4
replies
274
views
Adaptive sampling for whole chromosomes
T2T Nanopore AdaptiveSampling aneuploidy centromeres
15 days ago by njornet ▴ 20
0
votes
4
replies
318
views
Coverage observed in introns in the Knockdown genes but not in knockout genes
RNA-seq STAR IGV
28 days ago by rohitsatyam102 ▴ 850
2
votes
4
replies
1.4k
views
How to fix Error in dat[, batch == batch_level] : (subscript) logical subscript too long when removing batch effects
microarray combat batch-effect median-normalization
updated 7 days ago by 43k • written 18 months ago by • 0
1
vote
4
replies
389
views
what is the normal range of htseq-count output for homo sapiens RNA-Seq
Transcriptomics htseq-count RNA-Seq NGS hisat2
updated 13 days ago by ★ 1.7k • written 14 days ago by • 0
1
vote
4
replies
1.3k
views
Splitting long reads into shorter chunks
long-read
updated 20 days ago by 43k • written 5.8 years ago by ▴ 60
0
votes
4
replies
249
views
different FeatureCounts output for the same data
fpkm Counts Rsubread rna-seq
1 day ago by sehriban.buyukkilic ▴ 10
1
vote
4
replies
2.2k
views
Remove batch effect for prediction of RNA-seq data
RNA-Seq batch-effect Random-Forest
updated 8 days ago by 43k • written 4.7 years ago by ▴ 10
0
votes
4
replies
402
views
Is it reasonable to discard reads that show variation of quality across its length?
Trimming
28 days ago by BRENO • 0
0
votes
4
replies
1.8k
views
Correcting batch effect in unevenly distributed groups
RNA-Seq batch-effect R
updated 8 days ago by 43k • written 4.8 years ago by ▴ 20
2
votes
4
replies
2.6k
views
DESeq2 inconsistent results
differential-gene-expression RNA-Seq DESeq2
updated 16 days ago by 43k • written 8.1 years ago by ▴ 80
2
votes
4
replies
303
views
Number of CPUs to use by DRAP for transcriptomic assmbly
DRAP CPU transcriptomics
27 days ago by Mohamed Abderrahmane ▴ 20
1
vote
4
replies
280
views
Removing batch effect using combat-seq
batch effect RNA-Seq combat-seq
updated 24 days ago by ★ 1.7k • written 25 days ago by • 0
0
votes
4
replies
577
views
Per base sequence content failed miserably
fastqc sequence trimmomatic NGS assembly
7 days ago by Kai Xin • 0
0
votes
4
replies
332
views
What is the samtools flag used in bamPEFragment?
deeptools
updated 14 days ago by 141k • written 17 days ago by • 0
2
votes
4
replies
260
views
interpretartion of a vcf file
calling genotype ONT variant diploid
2 days ago by samuelkalandarov2002 ▴ 10
4
votes
4
replies
359
views
Average expression of a sample in single-cell data
single-cell rna-seq
23 days ago by newuser2024 • 0
1
vote
4
replies
365
views
Molecular docking with Autodock
Docking proteomics
updated 20 days ago by 43k • written 12 weeks ago by ▴ 10
2
votes
4
replies
316
views
SnpEff annotates coding duplication as intronic?
snpeff
9 days ago by kirill.zaslavsky • 0
0
votes
4
replies
1.1k
views
Getting biological replicates from SRA run NCBI
fastq AWS SRA RNAseq
24 days ago by Andres ▴ 20
1
vote
4
replies
2.8k
views
removing confounding batch effect with RUVseq
RUVseq RNA-Seq batch-effect DESeq2
updated 8 days ago by 43k • written 5.1 years ago by ★ 2.6k
2
votes
4
replies
292
views
Addmetadata to seurat obj
seurat
15 days ago by synat.keam ▴ 100
1
vote
4
replies
344
views
How to get human-mouse conservation score from UCSC
conservation mouse IGV human score
20 days ago by diqixiaoyaoer ▴ 10
0
votes
4
replies
500
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx deconcolution
8 days ago by feather-W • 0
1
vote
4
replies
812
views
I want to calculate if the sample has whole genome duplication event or not?
sequencing wgs
16 days ago by Hyper_Odin ▴ 310
3
votes
4
replies
3.5k
views
any recommended tools for batch effect and normalization not written in R?
R RNA-Seq combat python batch-effect
updated 7 days ago by 43k • written 7.1 years ago by ▴ 310
3
votes
4
replies
353
views
Single cell analysis with "meta".tsv.gz file
Single-cell
23 days ago by Estevão • 0
1
vote
3
replies
246
views
some error in building kraken2 database
metagenome kraken2
2 days ago by Art1ess • 0
1
vote
3
replies
4.1k
views
Evaluating removing batch effect tools with PCA or MDS?
bioconductor limma sva r batch-effect
updated 7 days ago by 43k • written 7.6 years ago by ★ 1.2k
0
votes
3
replies
1.1k
views
Batch effect for SNP array
sva combat batch-effect SNP
updated 10 days ago by 43k • written 4.2 years ago by ▴ 10
526 results • Page 2 of 11
Recent Votes
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Simulation of label-free bottom-up proteomics expression dataset
How to normalize long-read RNA-seq data for comparison with short-reads
EdgeR analysis with CPM normalzed counts
Alternative splicing convention
cellular niches analysis with spatial transcriptome data in Seurat and Bioconductor
Answer: Seurat merge and batch correction
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Recent Replies
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File? by Jalil Sharif ▴ 80
The updated code in R using rtracklayer for reading a gtf file. https://github.com/jalilsharif/gtf_utr_fix_r/blob/main/gencode_utr_fix_d…
Answer: Rare Disease Variant Pathway Analysis by The_PyPanda ▴ 10
Thank you LauferVA, Your advice has been useful and I now a lot to think about and read. Also, I just wanted to clarify I do not ha…
Comment: CDS vs cDNA vs transcript for mapping RNA-Seq reads by Antonio R. Franco ★ 5.1k
You cannot do it with Kallisto either. In fact, the indexation will fail in attempting to index a genome file
Comment: PCA plot by ATpoint 82k
What is your question? Add details and clarity. Ask a precise question and please avoid opening more questions on the same underlying issue…
Comment: genome assembly records not present in assembly_summary.txt by Joe 21k
If you have the accession numbers can you not use something like `eutils`?
Comment: what is the purpose of indexing the reference genome (Kallisto) by ATpoint 82k
For question 1: For question 1: Purpose of indexing a genome/transcriptome/book/anything: https://www.biostars.org/p/212594/ For question …
Comment: Create a new bed file with all pairwise combinations between two other bed files by Pierre Lindenbaum 161k
> Next, I tried using bedtools window but in your original post you said > tried finding the intersection of these bed files using bedto…
Comment: How to trim transcripts using information from NCBI contamination screen report by Lada ▴ 30
Thank you very much! I tried it out! This is a handy tool useful for many different applications, and in regards to my problem - although …
Comment: Create a new bed file with all pairwise combinations between two other bed files by J • 0
Thank you for replying Pierre. I first added a third column to the SNP bed file, so that I would get a range of 1 for each SNP awk 'B…
Comment: Create a new bed file with all pairwise combinations between two other bed files by Pierre Lindenbaum 161k
> using bcftools Show us what you tried
Answer: gvcf joint calling by Jeremy Leipzig 22k
> Hi, guys, there is a question about the genomic gVCF file. I wonder > that since gVCF contains the non-var block records, why after merge…
Comment: Missing protein (VEGF-A) in String db by shalespringer • 0
Thank you for replying here; this helped me figure out why MAPK10 was missing from my results. It was also marked as a pseudogene in the En…
Comment: How to convert plink files to Hapmap Format by Sofia • 0
These are the first lines of the output: (Please is it normal to have NA in the P value column ?) CHR …
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie by atowns21 • 0
So I used the barcodes that I created (combos of positions 1-10 and 11-20) and I obtained similar alignment stats as the paper I pulled the…
Comment: How to convert plink files to Hapmap Format by Sofia • 0
Thank you so much, it actually worked!
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