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122,217 results • Page 725 of 2445
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1
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3
replies
1.2k
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Size factors upon collapsing replicates in RNA-seq analysis
RNA-Seq DESeq2 R
4.8 years ago by mickey_95 ▴ 110
20
votes
3
replies
5.2k
views
7 follow
Co-expression analysis at single cell level
rna-seq scRNA
updated 23 months ago by ▴ 10 • written 4.8 years ago by ▴ 60
0
votes
3
replies
1.3k
views
confusion with GSEA result with custome gene set
RNA-Seq enrichment GSEA
4.8 years ago by SJ Basu ▴ 60
1
vote
1
reply
969
views
Software/package that can visualise amino acid mutations against a reference genome
mutations visualisations
4.8 years ago by SaltedPork ▴ 170
3
votes
4
replies
2.1k
views
diferentially expressed ensembl ID to gene symbol conversion
DEG Ensembl HGNC_symbol biomart
4.8 years ago by imaparna27 ▴ 20
7
votes
6
replies
6.0k
views
Whole Genome Dna Amplification Before Applying Wgs
ngs dna snp indel qualitycontrol
updated 4.8 years ago by 20 • written 12.7 years ago by ▴ 770
0
votes
1
reply
832
views
circBase related query
circBase
4.8 years ago by harry ▴ 40
0
votes
0
replies
856
views
23andMe Internal I codes to RSID list?
SNP
4.8 years ago by r0bin.rt44 • 0
2
votes
3
replies
1.0k
views
Merging fastq files paird end
fastq
updated 4.8 years ago by 154k • written 4.8 years ago by ★ 4.4k
3
votes
3
replies
2.1k
views
How to plot alignment statistics; how many reads are mapped to the genome?
samtools RNA-Seq
4.8 years ago by anamaria ▴ 220
2
votes
12
replies
5.1k
views
Error: malformed header while uploading .vcf.gz files to Michigan imputation server
SNP software error
updated 4.8 years ago by 20 • written 6.3 years ago by • 0
6
votes
5
replies
3.5k
views
Forum: Pacific Bio Long Reads vs Illumina Short Reads
next-gen RNA-Seq alignment
updated 2.7 years ago by 45k • written 4.8 years ago by ▴ 70
1
vote
1
reply
1.3k
views
How to get information about antisense/sense lncRNAs?
RNA-Seq lncrna gencode
updated 4.8 years ago by ★ 19k • written 4.8 years ago by ▴ 140
10
votes
15
replies
15k
views
6 follow
cellranger count help
RNA-Seq 10x
updated 4.8 years ago by ▴ 30 • written 5.7 years ago by ▴ 50
0
votes
1
reply
984
views
VCF to bcf conversion; vcf file header missing
vcftools VCF
updated 2.7 years ago by 45k • written 4.8 years ago by ▴ 10
0
votes
3
replies
1.2k
views
How can I get a count of mRNA + lncRNAs from Gencode + lncipedia?
rna-seq lncRNA
4.8 years ago by njk639 • 0
1
vote
13
replies
8.3k
views
6 follow
DiffBind error when calling dba.count
ChIP-Seq
updated 11 weeks ago by ▴ 10 • written 5.5 years ago by ▴ 170
1
vote
4
replies
1.8k
views
How to improve the alignment performance in targeted sequencing data
DNA-seq targeted-sequencing alignment
updated 4.8 years ago by 15k • written 4.8 years ago by ▴ 10
3
votes
8
replies
1.8k
views
Merging .fq files per sample using a big loop - BASH?
fastq bash genomics
updated 2.7 years ago by 45k • written 4.8 years ago by ▴ 30
0
votes
1
reply
715
views
how to use EUPAN whith assembled genomes
genome Assembly
updated 4.8 years ago by 20 • written 4.8 years ago by • 0
0
votes
1
reply
769
views
About peptide design
software error
updated 4.8 years ago by ★ 30k • written 4.8 years ago by • 0
4
votes
1
reply
59k
views
ggmaplot error: Unlabeled data points (too many overlaps). Consider increasing max.overlaps
MAplot r ggplot2 ggmaplot
updated 4.3 years ago by 90k • written 4.8 years ago by ▴ 110
0
votes
0
replies
1.2k
views
Job: APHL-CDC Newborn Screening Bioinformatics and Data Analytics Fellowship
R genome next-gen
updated 2.5 years ago by 45k • written 4.8 years ago by • 0
0
votes
4
replies
3.3k
views
How to remove duplicate SNP IDs from VCF files?
SNP genome sequence
updated 4.8 years ago by ★ 90k • written 4.8 years ago by ▴ 270
1
vote
0
replies
1.8k
views
News: 3-day ONLINE TRAINING - NEXTFLOW
workflow Nextflow
updated 2.8 years ago by 45k • written 4.8 years ago by ★ 2.7k
5
votes
7
replies
2.4k
views
compiling shapeit4 : cannot find -lcurl
software error compiling
updated 4.8 years ago by 13k • written 4.8 years ago by 2.9k
0
votes
0
replies
1.5k
views
Bismark low mapping efficiency
Bismark WGBS mapping methylome
4.8 years ago by mailard ▴ 30
8
votes
6
replies
34k
views
6 follow
Where To Download Hg19 Gene Annotation, Transcript Annotation And Cdna Fasta Files?
hg19 ucsc
updated 2.9 years ago by 45k • written 12.4 years ago by ▴ 100
0
votes
9
replies
1.9k
views
Adapter sequences in RNA-seq
RNA-Seq sequencing next-gen
4.8 years ago by artgrigorov ▴ 30
0
votes
4
replies
2.0k
views
Bus Error When Using Bedtools Coverage
bedtools bedtoolscoverage bus error
updated 4.8 years ago by ▴ 10 • written 5.0 years ago by • 0
1
vote
1
reply
947
views
Whole Exome sequenincg Variant Priortization
NGS WES WGS Variant Priortization
updated 4.8 years ago by • 0 • written 4.8 years ago by ▴ 100
0
votes
0
replies
922
views
MEGA only Analyzing First Sequence
Mega .meg software error .mas analyze
updated 4.8 years ago by 20 • written 4.8 years ago by • 0
0
votes
0
replies
582
views
Population Structure Analysis with hybridLab
SNP hybridSimulation
4.8 years ago by safiq713 ▴ 10
0
votes
7
replies
1.9k
views
subread keeps makes a weird .sam file, have i done something wrong?
subread rsubread alignment DNA reference
4.8 years ago by hello_bioinf ▴ 250
1
vote
0
replies
1.2k
views
TCGA methylation data analysis. beta values to differentially regulated CpGs
methylation beta values DMP
4.8 years ago by english.server ▴ 300
0
votes
1
reply
2.0k
views
TORCH CUDA issue / cellpose
cuda gpu torch
updated 4.6 years ago by 27k • written 4.8 years ago by ▴ 120
3
votes
6
replies
2.4k
views
Filtering of transcripts with more than two exons
sequence RNA-Seq
updated 4.8 years ago by ▴ 480 • written 4.8 years ago by ▴ 10
0
votes
3
replies
1.4k
views
Mapping DNA position to Protein Position in E. Coli
gwas genomics sequencing
updated 2.7 years ago by 45k • written 4.8 years ago by ▴ 20
1
vote
2
replies
1.1k
views
No overlapping contigs found.
ChIP-Seq GATK
4.8 years ago by L_LANKA • 0
2
votes
2
replies
1.7k
views
Extract the position from a huge vcf file
vcf bcftools tabix
updated 4.8 years ago by 166k • written 4.8 years ago by ▴ 40
1
vote
3
replies
1.6k
views
Calculating fold change...CONFUSION
RNA-Seq Fold-change
updated 4.8 years ago by 105k • written 4.8 years ago by • 0
1
vote
2
replies
895
views
Combining bed files from targeted sequencing panels using Bedtools intersect
next-gen bedtools
updated 2.7 years ago by 45k • written 4.8 years ago by ▴ 10
0
votes
0
replies
815
views
Convert 70 VCF to PED and MAP plink files
plink vcf pca admixture
4.8 years ago by anithanagaraj93 ▴ 10
4
votes
5
replies
1.5k
views
should each RNA-seq has Circular RNA?
alignment RNA-Seq Circular RNA CIRI2
written 4.9 years ago by ▴ 170
1
vote
3
replies
1.6k
views
P3in file for primer3 : 0 records created
sequence misa primer3
4.8 years ago by avnim ▴ 10
0
votes
1
reply
1.2k
views
exon skipping and intron retention analyse
RNA-Seq alignment gene
updated 4.7 years ago by • 0 • written 4.8 years ago by ▴ 440
0
votes
0
replies
726
views
Gapfiller creates more mismatches than SSPACE. Why?
Assembly SSPACE genome GapFiller scaffolding
4.8 years ago by karenclarom9 • 0
0
votes
1
reply
1.4k
views
scRNA DE Analysis
scran scRNA DE
updated 4.8 years ago by ★ 19k • written 4.8 years ago by • 0
3
votes
1
reply
6.3k
views
Subsetting anndata on basis of louvain clusters
python scanpy anndata R RNA-Seq
updated 4.8 years ago by ▴ 20 • written 5.2 years ago by ▴ 70
1
vote
1
reply
998
views
Create pseudo-replicates by "evenly" splitting reads file?
RNA-Seq Assembly paired-end reads
4.8 years ago by Dunois ★ 2.9k
122,217 results • Page 725 of 2445
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what cause poly-G from NextSeq
what cause poly-G from NextSeq
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Recent Replies
Comment: Issue while running Kenddata. by GenoMax 154k
Look inside the `*.log` files to see if you can get additional clues (and post them here, if you can't figure out things). Check for lines …
Comment: Question about QC and scrublet by Arup Ghosh 3.5k
You can run Scrublet before filtering cells with high gene counts and compare the doublet score vs `n_counts_genes`.
Answer: How to perform GO enrichment in non-model organisms? by lieven.sterck 16k
In first instance you will as you say need to assign GOterms to your genes. eggNOG-mapper is certainly a valid approach to do this indeed. …
Comment: circos plot for genomic features by Matteo Ungaro ▴ 140
@colindaven thanks a lot! `clinker` also seems to be a nice/effective tool to do so. It happens we stuble across a work where they used `Ci…
Comment: circos plot for genomic features by colindaven 8.1k
Why not use something like Jbrowse2 instead ? https://jbrowse.org/jb2/gallery/ You can load both haplotypes, use minimap2 to create a paf …
Comment: How excactly is the Q30 is calculated? by colindaven 8.1k
This is really a question for your instrument provider. Only MGI application specialists and their bioinformaticians can really answer this…
Answer: How excactly is the Q30 is calculated? by GenoMax 154k
[**Phred quality scores**][1] have been in use since the 1990s and early days of human genome project. They were co-opted in the fastq form…
Comment: best practice for diploid variant calling by Matteo Ungaro ▴ 140
@kevin thanks I was experimenting with the following since I already pursued most of the approaches you mentioned and, in practice, they ar…
Answer: Chip-seq analysis Diffbind by ATpoint 90k
I think the results are expected. a) n=2 is underpowered, for any assay and in particular for ChIP-seq which has considerable noise. b) you…
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Wu-Sheng Zhang ▴ 10
Hi @arup , after changing the file name following the read length, I can process them using cellranger arc successfully. Thank you very muc…
Comment: Visualize methylation status in Pacbio Hifi read by cmdcolin ★ 4.4k
(as the JBrowse dev) I'm glad to hear this. if you see any trouble with it feel free to let me know, I have tried to keep up to date with m…
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Wu-Sheng Zhang ▴ 10
Got it! I will try to switch their name and re-run the cellranger arc. Thank you very much, @arup !
Answer: low quality data or file name swapping -- cellranger arc errors when processing by Arup Ghosh 3.5k
The barcode files with 24nt read length W71_LUNGrep2_S6_L001_R3_001.fastq.gz and W71_LUNGrep2_S6_L002_R3_001.fastq.gz should be the R2.
Comment: ID unifiying across different datasets by GenoMax 154k
Each database has their own method of annotation/validation. Depending on resources available there may be a lag between the databases in t…
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Wu-Sheng Zhang ▴ 10
Hi @arup , thank you very much for your suggestions, and here are the results -- they seems correct. May I have your suggestions? Thank you…
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