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1,000 results • Page 2 of 20
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6
votes
12
replies
2.0k
views
Help with error in cellranger
Cellranger
updated 11 months ago by 141k • written 11 months ago by ▴ 260
6
votes
6
replies
765
views
extract the original sequence from multiple sequence alignment (MSA)
MSA alignment
4 months ago by Ann ▴ 40
6
votes
3
replies
634
views
How can I adjust Y-axis scale when making relative abundance box plot ?
statistics box-plot R scale_adjustment logarithm
updated 4 months ago by ▴ 890 • written 4 months ago by ▴ 40
6
votes
2
replies
729
views
miRNA tool for search targets for genes
mirna targets
updated 10 months ago by 43k • written 2.8 years ago by ★ 1.2k
5
votes
6
replies
393
views
7 follow
Seeking Help with Unexpected MA Plot Output
MAplot RNAseq Rstudio
updated 23 days ago by 100k • written 24 days ago by • 0
5
votes
10
replies
1.3k
views
the distribution of log2Fc and t value are not similar for bulk RNA-seq
decoupleR RNA-seq
8 months ago by alwayshope ▴ 40
5
votes
8
replies
597
views
Multiple threads on ubuntu server
Ubuntu
updated 3 months ago by 6.4k • written 3 months ago by ▴ 50
5
votes
4
replies
1.2k
views
Converting Bam file to Fasta (Zipped)
bedtools samtools
updated 10 months ago by 43k • written 18 months ago by ▴ 350
5
votes
10
replies
848
views
Error when viewing a bam file
samtools
updated 10 months ago by 43k • written 12 months ago by ▴ 260
5
votes
4
replies
1.7k
views
Detection of DE genes among different tissues of an organism during time - RNA seq
detection DE-genes multi-treatments time-series
updated 11 months ago by 43k • written 7.8 years ago by ▴ 760
5
votes
4
replies
677
views
FASTQ to BAM to CRAM to FASTQ
Samtools
5 months ago by ManuelDB ▴ 80
5
votes
8
replies
1.0k
views
sc-RNA seq pipeline
scRNA-seq NGS RNA-Seq
3 months ago by subhiksha ▴ 30
5
votes
11
replies
1.3k
views
Interpret IGV output inversion
variant-calling IGV alignment
updated 8 months ago by ★ 3.8k • written 8 months ago by ▴ 300
5
votes
1
reply
682
views
Learning Linux advance commands
grep awk linux sed
updated 6 months ago by ▴ 60 • written 18 months ago by ▴ 140
5
votes
7
replies
1.4k
views
error while using cyvcf2 to parse the vcf file
cyvcf2 vcf htslib
updated 11 months ago by 43k • written 23 months ago by ▴ 140
5
votes
8
replies
1.9k
views
looking for tools to detect RNA contamination in DNA
RNA-Seq DNA-Seq contamination QC
updated 6 months ago by • 0 • written 3.7 years ago by ▴ 230
5
votes
3
replies
602
views
Strand bias in supplementary alignments from Nanopore
minimap2 nanopore strand
updated 5 months ago by ★ 3.8k • written 5 months ago by 14k
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
5
votes
6
replies
1.7k
views
Filter out Bam not overlapping with Bed File (keeping a read and its mate)?
samtools bam bed
updated 10 months ago by 43k • written 17 months ago by ▴ 350
5
votes
3
replies
349
views
samtools view: error reading file
samtools bowtie2
updated 7 weeks ago by ▴ 70 • written 7 weeks ago by • 0
5
votes
19
replies
4.0k
views
8 follow
Hisat2 aligner problem
RNA-Seq ChIP-Seq alignment Assembly software error
updated 4 months ago by 82k • written 4.9 years ago by ▴ 340
5
votes
2
replies
1.7k
views
Batch effects from sequencing samples accross multiple flow cells.
rna-seq batch batch-effect sequencing
updated 9 days ago by 43k • written 2.9 years ago by ▴ 60
5
votes
5
replies
1.8k
views
bio-newbie / gene research / tools and methods
methods research gene
updated 11 months ago by 43k • written 6.3 years ago by • 0
5
votes
5
replies
558
views
Generate BED file
bed
11 weeks ago by daffodil ▴ 10
5
votes
1
reply
679
views
Challenges in Variant Calling and Genotyping with Short-Read Data Mapped to a Pangenome Graph: Seeking Guidance
vg pggb giraffe
updated 6 months ago by ▴ 460 • written 6 months ago by ▴ 30
5
votes
3
replies
535
views
Visualisation of accessible regions in single cell atacseq data
visualization scATAC-seq single-cell
updated 7 months ago by 43k • written 7 months ago by ▴ 100
5
votes
7
replies
954
views
Are datasets for a unique cells, that downloded using sratoolkit?
RNA-Seq sequencing
updated 11 months ago by • 0 • written 4.3 years ago by ▴ 50
5
votes
2
replies
917
views
Recommended way to normalize SmartSeq2 gene expression matrix to better match 10X expression data
rna-seq smartseq2 r
updated 6 months ago by ▴ 70 • written 7 months ago by ▴ 10
5
votes
8
replies
1.9k
views
snpeff install error
snpeff
updated 11 months ago by 43k • written 12 months ago by ▴ 30
5
votes
3
replies
1000
views
abyss-pe genome assembly
konnector abyss-pe
updated 10 months ago by 43k • written 5.2 years ago by • 0
5
votes
5
replies
2.4k
views
Quickly retrieve reference genome sequence within python
sequence python
updated 5 months ago by ▴ 20 • written 5.6 years ago by ▴ 20
5
votes
6
replies
802
views
Calculate the percentage of genomic region covered from the BED file.
NGS sequencing genomics exome genes
updated 9 months ago by ▴ 900 • written 9 months ago by ▴ 40
5
votes
35
replies
3.6k
views
Reduce set of chromosomes in Pangenome graph
pangenome vg
updated 9 months ago by ▴ 460 • written 10 months ago by • 0
5
votes
7
replies
935
views
Salmon index not progressing
salmon
updated 7 months ago by 54k • written 7 months ago by ▴ 160
5
votes
11
replies
997
views
Make heatmap for RNA-seq with non replicate
RNA-seq
updated 8 months ago by 43k • written 8 months ago by ▴ 260
5
votes
1
reply
614
views
Enricher with Gene Symbols
DGE ClusterProfiler Enrich ORA
updated 8 months ago by ★ 2.3k • written 8 months ago by ▴ 100
5
votes
8
replies
3.7k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression RNA-seq gene-ontology
updated 16 days ago by 43k • written 6.5 years ago by ★ 1.6k
5
votes
7
replies
828
views
About the value in bigwig file
ATAC-seq
updated 9 months ago by ▴ 900 • written 9 months ago by ▴ 260
5
votes
8
replies
2.4k
views
SV calling using giraffe/vg
vg Giraffe calling structural variant
updated 9 months ago by ▴ 460 • written 15 months ago by • 0
5
votes
6
replies
1.4k
views
DESeqDataSetFromHTSeqCount function taking long time and utilizing more RAM
DESeq2 R RNA-Seq
updated 10 months ago by 43k • written 4.0 years ago by ▴ 90
5
votes
5
replies
640
views
Normalization and Genome-Wide Comparisons with Chipseq
chip-seq Chipseq Normalization
updated 4 months ago by ▴ 500 • written 4 months ago by ▴ 10
5
votes
5
replies
626
views
Counting 705 fasta header characters ('>') in human genome
human-genome genetics
updated 6 months ago by 82k • written 6 months ago by ▴ 10
5
votes
5
replies
513
views
Example MAF Files
MAF
updated 4 months ago by 43k • written 4 months ago by ▴ 120
5
votes
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression RNA-Seq GTex DESeq2
updated 16 days ago by 43k • written 6.4 years ago by ▴ 10
5
votes
7
replies
3.2k
views
8 follow
bwa mem -T (alignment score) not doing anything
SNP genome sequence
updated 6 months ago by 100k • written 5.9 years ago by ▴ 10
4
votes
3
replies
303
views
Should you remove PCR duplicates for kmer counting?
kmer dedup duplicates
updated 11 weeks ago by 4.6k • written 11 weeks ago by ▴ 30
4
votes
2
replies
470
views
KEGG DATABASE
DATABASE KEGG
updated 4 months ago by ★ 1.8k • written 4 months ago by • 0
4
votes
8
replies
2.0k
views
How to extract promoter sequences from a plant draft genome?
promoter genome
updated 10 months ago by 43k • written 4.6 years ago by ▴ 120
4
votes
4
replies
643
views
Feedback on mouse brain scRNA-seq quality control
mouse brain singe-cell scRNAseq quality-control
8 months ago by nshenoy ▴ 50
4
votes
2
replies
623
views
Visualization package for Maf Files using Python
Python maftools Visualization MAF
updated 6 months ago by ★ 1.5k • written 6 months ago by ▴ 100
1,000 results • Page 2 of 20
Recent Votes
Comment: Sequence read length shorter than flow cell specification
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
Detecting somatic variants in non-tumor tissue without normals
Answer: Sequence read length shorter than flow cell specification
Answer: Sequence read length shorter than flow cell specification
Comment: Why gatk VariantAnnotator required bam and coverage files
A: Generate Vcf.Gz File And Its Index File Vcf.Gz.Tbi
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Recent Replies
Answer: Sequence read length shorter than flow cell specification by swbarnes2 14k
The company probably had you share your run with someone who needed the extra bases. So you get the extra bases free. Just use them unle…
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix by Ram 43k
Thank you, the `csvtk spread` is super useful. I usually import into R using `lapply` then `Reduce` using `merge` but this might be easier.
Comment: Annovar using R package by DKA ▴ 40
Thank you for your guidance. The thing is that I am unfamiliar with using such environments, unfortunately.
Comment: Treatment VS Control in Single Cell RNAseq analysis by ATpoint 82k
Open a new question, with details.
Comment: Normalize scRNAseq data to housekeeping genes to compare several datasets by ATpoint 82k
I recommend https://bioconductor.org/books/3.18/OSCA.basic/normalization.html as well as the "advanced" section in this book.
Comment: Why gatk VariantAnnotator required bam and coverage files by QX • 0
thank you!
Comment: Treatment VS Control in Single Cell RNAseq analysis by kilcdincer ▴ 10
Hello, I have more or less same experimental setting and was wondering how you proceeded with your analysis? Can I reach its GitHub reposit…
Comment: BLAST using both nucleotides and taxonomic local databases by GenoMax 141k
> I ask this as some BLAST command fields as scinames or sblastnames do not give any output with a classic nt BLAST If that information is…
Answer: BLAST using both nucleotides and taxonomic local databases by 5heikki 11k
This has been discussed [many times][1] [1]: https://www.biostars.org/p/76551/
Answer: why renaming Idents in Seurat object doesn't work? by Bioinfotec ▴ 10
I think when you give indent to seuObj : ```r Idents(seuObj) <- 'RNA_snn_res.0.1' ``` You may wrongly assign other value to it such as `…
Answer: ScRNAseq-How to correctly choose cell type marker genes by Bioinfotec ▴ 10
In fact, there is no gold standard for cell type annotation. To achieve correct cell type classification, you can combine the two methos. F…
Answer: ScRNA data question by Bioinfotec ▴ 10
In violin plot, a dot represents a cell. Actually, the straight lines you see in your infected image just means these cells have the same e…
Comment: Sequence read length shorter than flow cell specification by GenoMax 141k
> the have sent data with different sequencing read lengths: 55bp pair ended and 80bp single ended If they sent data that is not what you…
Comment: How to know synonymous and non-synonymous SNPs from transcriptome sequencing by rohitsatyam102 ▴ 850
I have some off-the-chart dN/dS values for few genes (>20) when using your script on VCF obtained from a 20K plasmodium genomes (pf7K). | …
Answer: Sequence read length shorter than flow cell specification by ATpoint 82k
It is the amount of reagent in the kit that determines read length. Sometimes index cycle reagents are allocated to R1/R2 or they used anot…
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