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0
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233
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Choosing background for ORA using scrnaseq
scRNA-seq RNA-seq ORA
updated 19 days ago by 40k • written 21 days ago by ▴ 750
2
votes
1
reply
229
views
Producing Bulk samples from 10X data
rnaseq scrnaseq deseq2 bulk seurat
updated 21 days ago by 77k • written 21 days ago by ▴ 750
1
vote
5
replies
569
views
CellRanger output more cells than specified using --force-cells? Why?
scRNA-seq cellranger
25 days ago by rohitsatyam102 ▴ 750
0
votes
1
reply
342
views
bcftools unable to tag poor variant calls properly
bcftools gatk vafator
updated 3 months ago by 40k • written 7 months ago by ▴ 750
0
votes
3
replies
754
views
Tool to combine Germline Variant call from different variant callers
haplotypecaller gatk snps
7 months ago by rohitsatyam102 ▴ 750
0
votes
0
replies
272
views
Queries regarding SARS-CoV2 GISAID Genomes Submission
wf-artic COVID GISAID
10 months ago by rohitsatyam102 ▴ 750
5
votes
5
replies
1.2k
views
how to pass trimmed fastP output to bwa in Nextflow
fastp bwa nextflow
11 months ago by rohitsatyam102 ▴ 750
0
votes
4
replies
786
views
convert a list of plotly plots to an HTML output
ggplot2 bam plotly coverage
updated 11 months ago by 13k • written 11 months ago by ▴ 750
4
votes
4
replies
1.5k
views
bcl2fastq dumps most of the reads as undetermined
bcl2fastq
11 months ago by rohitsatyam102 ▴ 750
2
votes
6
replies
2.3k
views
reduce space between X-axis ticks
R GSEA
11 months ago by rohitsatyam102 ▴ 750
0
votes
0
replies
271
views
Make parts of process run once and other parts as loop
nextflow sars nextclade covid
13 months ago by rohitsatyam102 ▴ 750
4
votes
2
replies
660
views
Nextflow printing help message even when params.help is false
nextflow align bwa alignment
13 months ago by rohitsatyam102 ▴ 750
0
votes
6
replies
937
views
Nextflow runs Successfully but output files are empty. How to debug?
nextflow bcftools
13 months ago by rohitsatyam102 ▴ 750
3
votes
3
replies
1.6k
views
Fastqc in nextflow run only one pair of fastq.gz file and not on all Fastq files
nextflow fastqc
updated 14 months ago by 77k • written 14 months ago by ▴ 750
3
votes
5
replies
1.7k
views
Using shell command in Nextflow DSL=2 for BWA mem aligner
nextflow alihnment align bwa
14 months ago by rohitsatyam102 ▴ 750
3
votes
1
reply
442
views
GO Term Analysis in scRNASeq data with low number of genes expressed
scrnaseq Seurat
updated 14 months ago by ★ 1.8k • written 14 months ago by ▴ 750
0
votes
0
replies
666
views
Interpreting the Jackstraw plot of Seurat
genomics seurat plot scrnaseq
19 months ago by rohitsatyam102 ▴ 750
4
votes
4
replies
2.1k
views
How to select nFeature parameter of SelectIntegrationFeatures function in Seurat
scrnaseq Seurat
18 months ago by rohitsatyam102 ▴ 750
0
votes
0
replies
377
views
How to update gff/gtf files after using Mauve Config Mover
assembly genome Mauve
19 months ago by rohitsatyam102 ▴ 750
2
votes
3
replies
1.1k
views
Quick questions about Alevin and AlevinQC
alevinqc alevin
updated 2.0 years ago by 77k • written 2.0 years ago by ▴ 750
2
votes
2
replies
682
views
How to use RINalyzer plugin in cytoscape
cytoscape RINalyzer networks
updated 2.2 years ago by ▴ 180 • written 2.2 years ago by ▴ 750
2
votes
8
replies
1.2k
views
Parsing Dates from Multiple Websites
R
updated 2.4 years ago by 21k • written 2.4 years ago by ▴ 750
0
votes
1
reply
1.6k
views
Which VCF's to use for BQSR in GATK
GATK BQSR next-gen-sequencing
updated 6 months ago by 40k • written 3.6 years ago by ▴ 750
0
votes
0
replies
579
views
MNAse-Seq Dataset for Different Cancer Types
Cancer bigwig Mnaseseq
updated 6 months ago by 40k • written 2.8 years ago by ▴ 750
0
votes
0
replies
545
views
RNAseq of rice is super weird
rna-seq RNA-Seq sequence genome
3.0 years ago by rohitsatyam102 ▴ 750
2
votes
1
reply
2.5k
views
What packages/tools are available to use SJ.out.tab file obtained from STAR
RNA-Seq R next-gen sequence rna-seq
updated 3.0 years ago by ▴ 10 • written 3.0 years ago by ▴ 750
3
votes
3
replies
1.0k
views
Does it matters whether we give FASTA or FASTq files to STAR
RNA-Seq rna-seq alignment
updated 3.0 years ago by 13k • written 3.0 years ago by ▴ 750
5
votes
6
replies
707
views
Will it be fine if the benchmarking of an assembler/aligner is performed using a single chromosome of Human
assembly sequence alignment genome next-gen
updated 3.0 years ago by 13k • written 3.0 years ago by ▴ 750
4
votes
4
replies
1.4k
views
What tools/ commands must be used for time and memory usage estimation of an aligner
alignment assembly next-gen
updated 3.1 years ago by ▴ 980 • written 3.1 years ago by ▴ 750
1
vote
2
replies
1.1k
views
Processing GFF file for feature extraction
assembly sequence Assembly gene
3.1 years ago by rohitsatyam102 ▴ 750
0
votes
0
replies
567
views
EULER-SR throws error NULL was not declared in this scope
assembly
updated 3.1 years ago by 34k • written 3.1 years ago by ▴ 750
7
votes
10
replies
1.4k
views
How to download lakhs of abstracts in Batch for text mining study
R gene
3.1 years ago by rohitsatyam102 ▴ 750
0
votes
2
replies
765
views
From where to download human proteome atlas raw data
RNA-Seq
updated 3.2 years ago by ▴ 240 • written 3.2 years ago by ▴ 750
0
votes
0
replies
428
views
From Where to get tagSNPs file?
R gene bioconductor
updated 3.2 years ago by 11k • written 3.2 years ago by ▴ 750
0
votes
1
reply
914
views
DEXSeq gives most of the reads as "_empty"
DexSeq RNA-Seq next-gen alignment software error
updated 3.2 years ago by 20 • written 3.4 years ago by ▴ 750
1
vote
1
reply
831
views
Help required to understand Hi-C data and its Usage
Hi-C
updated 6 months ago by 40k • written 3.2 years ago by ▴ 750
0
votes
6
replies
894
views
How to find if our enhancer gene pair fall within TAD
sequencing R genome gene
updated 3.2 years ago by ▴ 680 • written 3.2 years ago by ▴ 750
5
votes
2
replies
1.6k
views
What does minoverlap = 1L means?
gene R annotatr
updated 3.2 years ago by 77k • written 3.2 years ago by ▴ 750
2
votes
3
replies
494
views
Genomics regions that common to atleast 10 cell types
bedtools bedops genome bed sequence
updated 6 months ago by 40k • written 3.3 years ago by ▴ 750
5
votes
7
replies
1.6k
views
DEXSeq aggregates two different genes together
dexseq RNA-Seq rna-seq
updated 3.4 years ago by 86k • written 3.4 years ago by ▴ 750
6
votes
7
replies
968
views
TERF2 shRNA silencing is visible in WB and qPCR but not reflected in PE RNASeq
RNA-Seq rna-seq genome next-gen
3.4 years ago by rohitsatyam102 ▴ 750
1
vote
3
replies
1.1k
views
Confusion regarding 7th and 8th column of FANTOM5 Enhancer Coordinates BED File
enhancer genome alignment
3.5 years ago by rohitsatyam102 ▴ 750
1
vote
5
replies
1.3k
views
How to correctly generate alignment Stat in RNA-Seq
RNA-Seq sequencing alignment rna-seq
updated 3.6 years ago by ▴ 50 • written 3.6 years ago by ▴ 750
2
votes
3
replies
948
views
Ambiguous fields in FANTOM 5 Enhancer_TSS_association.bed file
RNA-Seq gene genome
updated 3.7 years ago by ▴ 550 • written 3.7 years ago by ▴ 750
1
vote
2
replies
868
views
Sorting the BEd File
genome gene next-gen
updated 3.8 years ago by 20 • written 3.8 years ago by ▴ 750
0
votes
0
replies
517
views
From where to get Sub-telomeric Region Coordinates/ sequences for each chromosome
genome gene assembly Assembly ChIP-Seq
3.8 years ago by rohitsatyam102 ▴ 750
2
votes
1
reply
442
views
Greedy-Non greedy Pattern search
genome
3.9 years ago by rohitsatyam102 ▴ 750
7
votes
7
replies
1.5k
views
Different number of peaks between biological replicates?
sequencing ChIP-Seq replicates
updated 3.9 years ago by ★ 1.1k • written 3.9 years ago by ▴ 750
2
votes
3
replies
1.1k
views
MACS2 "total fragments in treatment" gives less number of fragments than expected
ChIP-Seq next-gen genome
3.9 years ago by rohitsatyam102 ▴ 750
4
votes
5
replies
3.4k
views
Which one to use for ChipSeq replicate comparison: Spearman or Pearson
ChIP-Seq correlation replicates genome
updated 3.9 years ago by ★ 1.1k • written 3.9 years ago by ▴ 750
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