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1,000 results • Page 2 of 20
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5
votes
6
replies
1.4k
views
DESeqDataSetFromHTSeqCount function taking long time and utilizing more RAM
DESeq2 R RNA-Seq
updated 11 months ago by 43k • written 4.1 years ago by ▴ 90
5
votes
7
replies
986
views
Salmon index not progressing
salmon
updated 7 months ago by 54k • written 8 months ago by ▴ 160
5
votes
5
replies
605
views
Generate BED file
bed
3 months ago by daffodil ▴ 10
5
votes
5
replies
327
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
11 days ago by Chris ▴ 280
5
votes
11
replies
1.4k
views
Interpret IGV output inversion
variant-calling IGV alignment
updated 9 months ago by ★ 3.8k • written 9 months ago by ▴ 300
5
votes
5
replies
674
views
Normalization and Genome-Wide Comparisons with Chipseq
chip-seq Chipseq Normalization
updated 5 months ago by ▴ 500 • written 5 months ago by ▴ 10
5
votes
19
replies
4.1k
views
8 follow
Hisat2 aligner problem
RNA-Seq ChIP-Seq alignment Assembly software error
updated 4 months ago by 82k • written 5.0 years ago by ▴ 340
5
votes
2
replies
957
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 8 months ago by ▴ 10
5
votes
8
replies
664
views
Multiple threads on ubuntu server
Ubuntu
updated 4 months ago by 6.4k • written 4 months ago by ▴ 50
5
votes
8
replies
2.0k
views
looking for tools to detect RNA contamination in DNA
RNA-Seq DNA-Seq contamination QC
updated 7 months ago by • 0 • written 3.8 years ago by ▴ 230
5
votes
11
replies
1.0k
views
Make heatmap for RNA-seq with non replicate
RNA-seq
updated 9 months ago by 43k • written 9 months ago by ▴ 280
5
votes
6
replies
1.8k
views
Filter out Bam not overlapping with Bed File (keeping a read and its mate)?
samtools bam bed
updated 11 months ago by 43k • written 18 months ago by ▴ 350
5
votes
8
replies
3.7k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression RNA-seq gene-ontology
updated 5 weeks ago by 43k • written 6.6 years ago by ★ 1.6k
5
votes
8
replies
1.1k
views
sc-RNA seq pipeline
scRNA-seq NGS RNA-Seq
4 months ago by Researcher ▴ 30
5
votes
5
replies
660
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
7
replies
3.2k
views
8 follow
bwa mem -T (alignment score) not doing anything
SNP genome sequence
updated 7 months ago by 100k • written 5.9 years ago by ▴ 10
5
votes
2
replies
1.8k
views
Batch effects from sequencing samples accross multiple flow cells.
rna-seq batch batch-effect sequencing
updated 4 weeks ago by 43k • written 3.0 years ago by ▴ 60
5
votes
1
reply
702
views
Challenges in Variant Calling and Genotyping with Short-Read Data Mapped to a Pangenome Graph: Seeking Guidance
vg pggb giraffe
updated 7 months ago by ▴ 460 • written 7 months ago by ▴ 30
5
votes
7
replies
974
views
Are datasets for a unique cells, that downloded using sratoolkit?
RNA-Seq sequencing
updated 12 months ago by • 0 • written 4.4 years ago by ▴ 50
5
votes
7
replies
501
views
RNA seq analysis
DESeq RNA-seq
4 days ago by Jacek ▴ 20
5
votes
8
replies
2.5k
views
SV calling using giraffe/vg
vg Giraffe calling structural variant
updated 10 months ago by ▴ 460 • written 16 months ago by • 0
5
votes
4
replies
746
views
FASTQ to BAM to CRAM to FASTQ
Samtools
6 months ago by ManuelDB ▴ 80
5
votes
3
replies
1.0k
views
abyss-pe genome assembly
konnector abyss-pe
updated 11 months ago by 43k • written 5.3 years ago by • 0
5
votes
4
replies
1.2k
views
Converting Bam file to Fasta (Zipped)
bedtools samtools
updated 11 months ago by 43k • written 19 months ago by ▴ 350
5
votes
10
replies
883
views
Error when viewing a bam file
samtools
updated 11 months ago by 43k • written 12 months ago by ▴ 280
5
votes
3
replies
561
views
Visualisation of accessible regions in single cell atacseq data
visualization scATAC-seq single-cell
updated 8 months ago by 43k • written 8 months ago by ▴ 100
5
votes
7
replies
874
views
About the value in bigwig file
ATAC-seq
updated 10 months ago by ▴ 900 • written 10 months ago by ▴ 280
5
votes
6
replies
846
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
1
reply
1.8k
views
How does FindNeighbors() and FindClusters() related and work?
seurat clustering
updated 9 months ago by ★ 2.5k • written 9 months ago by ▴ 120
5
votes
5
replies
7.3k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq bulk-RNASeq RNA-Seq single-cell
updated 5 weeks ago by • 0 • written 3.8 years ago by ★ 1.8k
5
votes
1
reply
693
views
Learning Linux advance commands
grep awk linux sed
updated 7 months ago by ▴ 60 • written 19 months ago by ▴ 140
5
votes
1
reply
645
views
Enricher with Gene Symbols
DGE ClusterProfiler Enrich ORA
updated 9 months ago by ★ 2.5k • written 9 months ago by ▴ 100
5
votes
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression RNA-Seq GTex DESeq2
updated 5 weeks ago by 43k • written 6.5 years ago by ▴ 10
5
votes
5
replies
2.5k
views
Quickly retrieve reference genome sequence within python
sequence python
updated 6 months ago by ▴ 20 • written 5.6 years ago by ▴ 20
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
5
replies
554
views
Example MAF Files
MAF
updated 5 months ago by 43k • written 5 months ago by ▴ 120
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
3
replies
442
views
samtools view: error reading file
samtools bowtie2
updated 10 weeks ago by ▴ 70 • written 10 weeks ago by • 0
5
votes
3
replies
654
views
Strand bias in supplementary alignments from Nanopore
minimap2 nanopore strand
updated 6 months ago by ★ 3.8k • written 6 months ago by 14k
5
votes
6
replies
454
views
7 follow
Seeking Help with Unexpected MA Plot Output
MAplot RNAseq Rstudio
updated 6 weeks ago by 100k • written 6 weeks ago by • 0
4
votes
3
replies
332
views
Should you remove PCR duplicates for kmer counting?
kmer dedup duplicates
updated 3 months ago by 4.6k • written 3 months ago by ▴ 30
4
votes
2
replies
494
views
KEGG DATABASE
DATABASE KEGG
updated 5 months ago by ★ 1.8k • written 5 months ago by • 0
4
votes
11
replies
699
views
Remove X in row name with only number
GSVA
updated 3 months ago by 43k • written 3 months ago by ▴ 280
4
votes
4
replies
533
views
Correlation for ATAC-Seq and Chip-Seq
RNA-Seq Chip-Seq ATAC-Seq
11 weeks ago by qudrat.nii ▴ 10
4
votes
2
replies
591
views
Can I still remove ambient RNA if I do not have raw barcode-gene matrix?
SoupX
6 months ago by malonzm1 ▴ 20
4
votes
5
replies
414
views
Filter out miRNA from ncRNA dataset
bowtie bowtie2 miRNA filtering ncRNA
updated 12 weeks ago by 82k • written 12 weeks ago by ▴ 10
4
votes
7
replies
636
views
DESeq2 Multifactor Design
RNA-seq DESeq2
updated 5 weeks ago by 43k • written 5 weeks ago by ▴ 20
4
votes
1
reply
596
views
How to Load a Molecular Signature Database into clusterProfiler gseGO?
ClusterProfiler RNA-seq GSEA
updated 10 months ago by ★ 1.6k • written 10 months ago by ▴ 100
4
votes
6
replies
926
views
Hisat2 index and alignment question
ubuntu rna-seq index hisat2
updated 7 months ago by 100k • written 7 months ago by • 0
4
votes
12
replies
7.9k
views
6 follow
BWA error: no ID within the read group line
bwa readgroups RG parallel
updated 3 months ago by ▴ 10 • written 3.4 years ago by ▴ 60
1,000 results • Page 2 of 20
Recent Votes
Interpreting the Jackstraw plot of Seurat
A: How is the design in DESeq2 work?
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
Answer: RNAseq coverage vs depth for transcript isoform expression?
constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
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Recent Replies
Answer: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from by ATpoint 82k
Use everything before the whitespace in list.txt, for example `A00869:294:HCW57DSXY:2:1101:3929:1000` and not `A00869:294:HCW57DSXY:2:1101:…
Answer: CellRanger output more cells than specified using --force-cells? Why? by scideas ▴ 30
I actually had this same issue with CellRanger v7- turns out that since you have 2 species in your mapping reference, CellRanger is forcing…
Answer: Checking chromosome builds for genotyping data by Muhammad • 0
Assume you have genotype data in Plink format. (G.bed, G.bim, G.fam) Download some reference panel data in Plink format (R.bed, R.bim, R.f…
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors) by nguyenn6 • 0
did you ever figure it out? i'm having the same issue.
Comment: Traveler with Infernal mapping failed by anton.i.petrov • 0
Hi Larissa! I am the lead developer of R2DT and I've just noticed this question. Could you please email help@r2dt.bio with your input seque…
Comment: constructing pangenome through psvcp by analyst ▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by GenoMax 142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
Comment: calculating genomic coverage/ base overlap in R by 1769mkc ★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks by ATpoint 82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner by Joe 21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression? by Gordon Smyth ★ 7.2k
See the exploration of isoform estimation precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167.…
Comment: How to handle duplicated genes in TCGA data? by txema.heredia ▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA by mavy ▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by hophuquy0944 • 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object by Alex Reynolds 35k
Yes, `bedmap` will perform operations on one or two BED files.
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