Limit : this month
all time today this week this month this year
930 results • Page 3 of 19
Sort: replies
Rank Views Votes Replies
7
votes
7
replies
6.0k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq SNP
updated 14 days ago by ▴ 850 • written 6.2 years ago by ▴ 10
10
votes
7
replies
7.1k
views
6 follow
Convert GVF to VCF
vcf
updated 23 days ago by • 0 • written 9.3 years ago by ▴ 970
0
votes
7
replies
131
views
Different output for read length
samtools BAM
updated 40 minutes ago by 161k • written 4 hours ago by ▴ 100
4
votes
7
replies
569
views
To get p-values for the TPM
P-value TPM RSEM
updated 14 days ago by ★ 6.0k • written 15 days ago by • 0
2
votes
7
replies
551
views
STARsolo ; Reads are NOT mapped to transcriptome
STARsolo
updated 28 days ago by 142k • written 4 weeks ago by • 0
0
votes
7
replies
1.9k
views
Batch effect correction in RNASeq data and plot Dendrograms cluster
clustering dendrogram RNA-Seq batch-effect
updated 21 days ago by 43k • written 4.0 years ago by ▴ 500
2
votes
7
replies
1.3k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq Salmon Isoseq
updated 10 days ago by ★ 7.1k • written 8 months ago by ▴ 10
1
vote
7
replies
474
views
Question regarding WGCNA
WGCNA Network-construction
5 hours ago by deepak • 0
0
votes
7
replies
6.1k
views
Pre-processing of RNA-Seq data for WGCNA
RNA-Seq WGCNA removeBatchEffect DESeq2
updated 22 days ago by 43k • written 7.7 years ago by ▴ 70
3
votes
7
replies
535
views
Integration of transcriptomics and proteomics: difficult matching names
rna-seq tmt nomenclature proteomics
23 days ago by ntsopoul ▴ 60
4
votes
7
replies
606
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity scVelo scRNA-seq splicing
10 days ago by e.r.zakiev ▴ 210
0
votes
7
replies
445
views
Applying the metacell2 algorithm using python
python single-cell scanpy metacell2
updated 1 day ago by ★ 2.0k • written 3 days ago by ▴ 140
1
vote
7
replies
457
views
Downsampling long-read BAM files
nanopore BAM QC ONT downsampling
6 days ago by eebloom ▴ 80
1
vote
7
replies
552
views
gvcf joint calling
WES GATK VCF gVCF
11 days ago by zihanss • 0
4
votes
7
replies
604
views
DESeq2 Multifactor Design
RNA-seq DESeq2
updated 25 days ago by 43k • written 26 days ago by ▴ 20
5
votes
6
replies
543
views
Programmatically retrieving positions of protein active site residues
Uniprot PDB Proteins
updated 9 days ago by ▴ 760 • written 10 days ago by ▴ 40
4
votes
6
replies
1.2k
views
Soft-clipping read ends based on read group
ancient molecule at bam DNA RG ends clipping damage
updated 1 day ago by ▴ 10 • written 2.5 years ago by • 0
0
votes
6
replies
481
views
Use of Kraken output for functional analysis
metagenomics kraken shotgun
updated 15 days ago by • 0 • written 5 weeks ago by ▴ 20
2
votes
6
replies
557
views
Correcting coordinates in gff3 file
awk unix gff3 python
updated 27 days ago by 4.6k • written 29 days ago by • 0
2
votes
6
replies
3.7k
views
Algorithm to remove batch effects
single-cell batch-effect RNA-Seq
updated 22 days ago by 43k • written 3.3 years ago by ▴ 80
3
votes
6
replies
2.0k
views
7 follow
DNA methylation preprocessing
SWAN DNA methylation Funnorm
updated 12 days ago by 43k • written 2.4 years ago by ▴ 10
0
votes
6
replies
2.1k
views
Copy number Variation analysis using conumee
R software error sequencing genome
updated 8 hours ago by 142k • written 3.2 years ago by ▴ 10
3
votes
6
replies
8.4k
views
RNA-seq, EdgeR and batch effects
RNA-Seq removeBatchEffect edgeR batch-effect
updated 22 days ago by 43k • written 9.4 years ago by ▴ 120
3
votes
6
replies
727
views
Ciriquant not configuring hisat2 indexed files
ciriquant
17 days ago by Atul K. • 0
0
votes
6
replies
426
views
Differential Expression Analysis using DESeq2 in R
deseq2 R
updated 5 days ago by 14k • written 6 days ago by • 0
3
votes
6
replies
905
views
Any problem re-using last year's RNA-Seq data in this year's analysis?
RNA-Seq batch-effect
updated 22 days ago by 43k • written 3.7 years ago by ▴ 20
0
votes
6
replies
504
views
Error in running Mauve alignner in Ubuntu 20.04
java linux aligner mauve
29 days ago by marongiu.luigi ▴ 710
8
votes
6
replies
2.6k
views
bwa 0.7.18 download to fix compile fail with GCC 10
bwa
updated 21 days ago by 3.0k • written 2.0 years ago by ▴ 230
10
votes
6
replies
10.0k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly rna-seq alignment
updated 13 days ago by ★ 5.1k • written 6.0 years ago by ▴ 510
10
votes
6
replies
14k
views
7 follow
How To Identify The 16S Rrna Gene Sequence In A Genome
updated 21 days ago by 6.4k • written 10.9 years ago by ▴ 10
0
votes
6
replies
608
views
PacBio adapters in transcriptome assembly from short read data?
adapter transcriptome sequencing pacbio vecscreen
24 days ago by Dunois ★ 2.5k
2
votes
6
replies
3.7k
views
Treatment VS Control in Single Cell RNAseq analysis
Single Cell RNAseq DE Analysis Treatment Control
updated 13 days ago by 82k • written 3.9 years ago by ▴ 280
4
votes
6
replies
1.5k
views
CompressedGRangesList don't have seqLengths: BiocParallel errors: Error in covRleFromGR(x, weight = weight, ignore.strand = ignore.strand): Seqlength…
gff3 GenomicRanges ORFik GenomicFeatures
updated 24 days ago by 142k • written 15 months ago by ▴ 30
1
vote
6
replies
490
views
Rename multiple fastq.gz files
fastq next-gen
updated 22 days ago by 8.5k • written 23 days ago by • 0
3
votes
6
replies
4.0k
views
Loading previously downloaded GEO SOfT data into R, using getGEO from GEOquery package
microarray r GEOquery
updated 22 days ago by 43k • written 5.0 years ago by ▴ 30
1
vote
6
replies
685
views
anRichment is missing
WGCNA anRichment
updated 3 days ago by 142k • written 5 months ago by ▴ 180
15
votes
6
replies
1.3k
views
6 follow
VCF to human friendly form?
vcf visualization
updated 24 days ago by 161k • written 20 months ago by ▴ 10
4
votes
6
replies
4.0k
views
Correcting for batch effect in RNA-seq data
RNA-Seq batch-effect
updated 22 days ago by 43k • written 4.8 years ago by ▴ 30
2
votes
6
replies
886
views
Batch effect correction with cell type enrichment analysis
limma RNA-seq r batch-effect
updated 22 days ago by 43k • written 19 months ago by ▴ 140
6
votes
6
replies
1.8k
views
agilent human all exon sureselct v7 bed file
exon human bed v7 agilent all sureselect
updated 4 days ago by ▴ 10 • written 24 months ago by • 0
7
votes
6
replies
1.3k
views
using different microarray datasets (meta-analysis?) for DEG pipeline
microarray meta-analysis DEG batch-effect
updated 22 days ago by 43k • written 4.9 years ago by ▴ 30
5
votes
6
replies
7.3k
views
scatter plot, aov()
aov scatter-plot anova
updated 22 days ago by 43k • written 3.2 years ago by ▴ 170
7
votes
6
replies
556
views
Filtering sam or bam file with maximum matching region
crisper-edited alignment match
18 days ago by analyst ▴ 50
1
vote
6
replies
358
views
Do I need to go back and filter my long-reads?
alignment nanopore filtering QC ONT
updated 6 days ago by 142k • written 24 days ago by ▴ 80
0
votes
6
replies
415
views
How to slice a gvcf file with tabix?
Tabix bed gvcf
16 days ago by Sd • 0
4
votes
6
replies
515
views
Odd results with BLAST remote
blast remote NCBI
updated 23 days ago by ▴ 180 • written 24 days ago by ▴ 150
2
votes
6
replies
5.2k
views
How to avoid over-correction by using harmony or CCA to batch correction in scRNA-seq?
scRNA-seq R seurat harmony batch-effect
updated 21 days ago by 43k • written 3.7 years ago by • 0
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq RNA-Seq exon
updated 3 days ago by ▴ 30 • written 6.7 years ago by ★ 1.2k
2
votes
6
replies
505
views
KEGG analysis in R
KEGG clusterProfiler Zea-mays
28 days ago by sansan_96 ▴ 80
1
vote
6
replies
1.6k
views
How can Differentially Expressed Genes be found by limma package after removing batch effect by ComBat function in sva package?
limma sva batch-effect R
updated 24 days ago by 43k • written 3.9 years ago by ▴ 10
930 results • Page 3 of 19
Recent Votes
course on Landscape Genomics at the EPFL in Lausanne (June 17-21)
course on Landscape Genomics at the EPFL in Lausanne (June 17-21)
cellranger error message
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
Network plot from expression data in R using igraph
Comment: RNA seq analysis
RNA seq analysis
Recent Locations • All
Canada, 2 minutes ago
Turkey, 3 minutes ago
United States, 4 minutes ago
United States, 4 minutes ago
United States, 5 minutes ago
United States, 6 minutes ago
São Paulo, 7 minutes ago
Recent Awards • All
Commentator to andres.firrincieli 3.6k
Scholar to tim.booth ▴ 50
Popular Question to strive • 0
Popular Question to LauferVA 4.2k
Popular Question to ManuelDB ▴ 80
Popular Question to nkls063408 • 0
Popular Question to rj.rezwan • 0
Recent Replies
Comment: Different output for read length by Pierre Lindenbaum 161k
the first read as a length of 1747, i wonder how you can just find '50' $ wget -qO - "https://gist.githubusercontent.com/Macdot3/4650…
Comment: Problem with Seurat package in PercentageFeatureSet function by bk11 ★ 2.4k
Yes, `CreateAssayObject` function is used for only expression matrix.
Comment: Different output for read length by marco.barr ▴ 100
Here is my result, I hope you can see it. [https://gist.github.com/Macdot3/4650243a10540d8c06f728ffc16a136c][1] [1]: https://gist.gith…
Comment: Different output for read length by marco.barr ▴ 100
I just published my link on paste, why can't I see my public paste on the site?
Comment: cellranger error message by Max • 0
I'm having a similar issue. The sample_id matches the filename prefix before _S1_L001, but I get the error: Log message: Requested sample(s…
Comment: Different output for read length by marco.barr ▴ 100
Thanks so much GenoMax, I'm sharing the link as you told me
Comment: Different output for read length by GenoMax 142k
Post the data at pastebin.com and add a link here or you could a GitHub gist. You were suspended by biostars SPAM bot since you pasted link…
Comment: Different output for read length by GenoMax 142k
Post the data at pastebin.com and add the link here. You were suspended by biostars SPAM bot since you pasted these links in quick successi…
Comment: RNA seq analysis by s.ghazala • 0
Could you clarify on what exactly you are referring to with "SRA data table". If you are retrieving fastq files (raw data), then you could …
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA by sovrappensiero ▴ 100
Thanks, Chris. I really appreciate your help. This has clarified a lot for me!
Answer: Snakemake fails to find conda in PBS by tim.booth ▴ 50
Snakemake does not have support for micromamba. There is an open issue: https://github.com/snakemake/snakemake/issues/2322
Comment: absolute path for symbolic links in Snakefile by tim.booth ▴ 50
Further to this answer - if you are using GNU coreutils (ie. any modern Linux), there is a "-r" flag to fix this problem. I typically use "…
Answer: Different output for read length by Pierre Lindenbaum 161k
I supect your reads are hard clipped. Show us the first lines of samtools view /home/sorted.bam | cut -f 2,6,10 | head -n 20
Comment: Presence of unknown sites in ANNOVAR output file by sainavyav22 • 0
Here you go. 1.perl convert2annovar.pl -format vcf4old 1008_Tumor.vcf > 1008Tumor_variant.avinput 2.perl annotate_variation.pl 100…
Comment: Filtering Multi-sample VCF file for all except one Genotype by Jeremy Leipzig 22k
Those are samples. If a sample has a 0/1 or a 1/1 genotype for that variant, they have the variant. Your question is ambiguous because you…
Traffic: 2625 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6