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122,213 results • Page 707 of 2445
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0
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471
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.geo file for a SAMOVA analysis
gene SAMOVA
4.7 years ago by ally • 0
2
votes
3
replies
8.7k
views
Adding extra labels (lines and text) in pheatmap R
RNA-Seq R pheatmap code
updated 4.7 years ago by ★ 1.8k • written 4.7 years ago by ▴ 390
0
votes
0
replies
983
views
Job: Job: CRISPR Microbiome Bioinformatician
bioinformatician CRISPR denmark microbiome
updated 2.3 years ago by 45k • written 4.7 years ago by • 0
1
vote
4
replies
1.6k
views
Malformed BAM while running GATK
GATK BAM Read group Barcode
4.7 years ago by shivangi.agarwal800 ▴ 120
3
votes
9
replies
2.7k
views
Merging position of all different CDS of a single gene in one line
CDS GFF gene duplication
updated 4.7 years ago by 20 • written 7.2 years ago by ▴ 60
6
votes
5
replies
6.5k
views
How to convert gvcf file to normal vcf file ?
vcf gatk gvcf
2.6 years ago by DareDevil ★ 4.5k
0
votes
1
reply
759
views
What is the diffecence between SMART-seq2 & Smart-seq2 protocol in single cell analysis?
RNA-Seq rna-seq sequencing next-gen
4.7 years ago by atulchandrasingha • 0
0
votes
1
reply
808
views
Genome sequence upload from NCBI in galaxy for RNA-seq data analysis
RNA-Seq next-gen alignment genome
4.7 years ago by microorganism_001 ▴ 30
0
votes
3
replies
1.1k
views
Annotation with KEGGrest
RNA-Seq
updated 4.7 years ago by 103k • written 4.7 years ago by • 0
2
votes
2
replies
1.2k
views
DE Analysis on Scran-Normalized Counts
R RNA-Seq scRNA-Seq
updated 4.7 years ago by 20 • written 4.8 years ago by • 0
4
votes
4
replies
1.8k
views
Conserved amino acids at active site of an enzyme
alignment evolution
updated 4.7 years ago by ★ 30k • written 4.7 years ago by • 0
0
votes
1
reply
1.1k
views
DiffBind with duplicates
DiffBind ChIP-Seq
4.7 years ago by jc2842 • 0
51
votes
15
replies
75k
views
15 follow
Any Recommendations For Software For Drawing Plasmid Maps?
visualization software
updated 3.6 years ago by 45k • written 14.5 years ago by ▴ 70
0
votes
1
reply
866
views
How to remove symol name in Gviz?
Gviz
updated 4.7 years ago by 45k • written 4.7 years ago by ▴ 30
3
votes
6
replies
2.6k
views
Command line Taxa search within SRA / NCBI Trace
SRA Taxa Taxonomic taxonomy
updated 3.9 years ago by • 0 • written 4.7 years ago by ▴ 10
2
votes
2
replies
998
views
Differences between codon usage bias vs. differential transcript usage (DTU)
codon transcription dtu genome splicing
updated 4.7 years ago by ★ 30k • written 4.7 years ago by • 0
0
votes
0
replies
1.2k
views
cuffmerge gtf_to_sam error?
assembly cufflinks cuffmerge gtf_to_sam
4.7 years ago by debitboro ▴ 270
0
votes
3
replies
840
views
ps_scan pfscan: Syntax error: "(" unexpected
gene sequence genome Assembly rna
updated 4.7 years ago by 45k • written 4.7 years ago by • 0
0
votes
1
reply
1.3k
views
nextflow picard markduplicates fatal error
nextflow picard markduplicates
4.7 years ago by loum • 0
9
votes
13
replies
2.9k
views
Error in raw count file of .sam after alignment on GRCh38
RNA-Seq Assembly alignment sequencing
updated 4.7 years ago by 20 • written 8.6 years ago by • 0
3
votes
4
replies
1.2k
views
Extracting sequencing data from SRA accesion
rna-seq next-gen sequence
updated 4.7 years ago by ▴ 80 • written 4.7 years ago by ▴ 10
0
votes
0
replies
893
views
DESeq2 assay weights usage
deseq zinb-wave RNA-Seq rna-seq deseq2
4.7 years ago by prachitipprabhu • 0
0
votes
0
replies
612
views
Problem with GOChord function in GOplot
R RNA-Seq software error
4.7 years ago by dmitriylanshakov • 0
1
vote
1
reply
574
views
find sequence of HSP70i
sequencing
updated 4.7 years ago by ★ 30k • written 4.7 years ago by • 0
2
votes
7
replies
6.3k
views
FASTQC: overrepresented sequences
RNA-Seq
updated 4.7 years ago by ▴ 30 • written 4.7 years ago by • 0
1
vote
2
replies
1.1k
views
How to annotate unclassified proteins?
annotation
updated 4.7 years ago by ★ 30k • written 4.7 years ago by ▴ 30
28
votes
20
replies
23k
views
10 follow
Apple M1 processor for bioinformactics
software error RNA-Seq R genome sequence
updated 2.8 years ago by ★ 2.9k • written 5.0 years ago by ▴ 80
0
votes
2
replies
1.6k
views
plotCorrelation scatter plot ChIP-seq data
ChIP-Seq deepTools correlation
4.7 years ago by Marco Pannone ▴ 810
1
vote
1
reply
2.5k
views
PRSice on Imputation vcf.gz data; conversion of files
prisce imputation vcf plink bgen
updated 4.7 years ago by ★ 4.8k • written 4.7 years ago by • 0
0
votes
0
replies
660
views
sample size on Pearson's correlation
wgcna scale-free-topology coexpression Network
4.7 years ago by hubsnets ▴ 30
3
votes
4
replies
2.1k
views
Demultiplexing of Smart-Seq2 library using bcl2fastq
bcl2fastq smart-seq2 sequencing
4.7 years ago by gnomee ▴ 50
1
vote
3
replies
1.1k
views
How do you design primers with sequencing adapters to amplify CRISPR-edited regions?
primer-design crispr primer3
updated 4.7 years ago by • 0 • written 4.7 years ago by ▴ 10
0
votes
3
replies
2.6k
views
How can I make parsing big fasta with biopython SeqIO go faster?
fasta biopython seqio extract python
updated 4.7 years ago by 22k • written 4.7 years ago by ▴ 40
5
votes
3
replies
16k
views
The fonts and size of a tree displayed by ggtree
R
updated 4.7 years ago by ▴ 30 • written 7.6 years ago by ▴ 110
0
votes
2
replies
1.9k
views
read10X ERROR Seurat
read10x singlecell rna R seurat
updated 4.7 years ago by 13k • written 4.7 years ago by ▴ 20
0
votes
2
replies
1.3k
views
Annotation of results from CD-HIT web server
CD-HIT
updated 4.7 years ago by ★ 30k • written 4.7 years ago by • 0
0
votes
0
replies
745
views
What is the common lncRNA-target reference file with proper lncRNA gene name?
lncRNA gene sequencing genome sequence
4.7 years ago by Apex92 ▴ 320
2
votes
2
replies
1.8k
views
How to get `assembly-stats` command?
ubuntu stats assembly-stats assembly sequencing
updated 4.7 years ago by 16k • written 4.7 years ago by ▴ 20
1
vote
1
reply
597
views
some question about the NGS sequence
rna-seq
4.7 years ago by 972050141 • 0
0
votes
0
replies
617
views
Bulk download from CNGBdb?
cngb Assembly genome
4.7 years ago by matthewcrossie • 0
0
votes
1
reply
851
views
To retrive all sequences
Assembly
updated 4.7 years ago by 154k • written 4.7 years ago by • 0
0
votes
2
replies
1.2k
views
Modifying an annotation files after transgene insertion
transgene insertion gtf annotation
4.7 years ago by Assa Yeroslaviz ★ 1.9k
1
vote
3
replies
1.4k
views
how to annotate Circular RNA gene type?
RNA-Seq Circular RNA annotation
4.7 years ago by modarzi ▴ 170
3
votes
6
replies
3.0k
views
Covariate correction which data take for downstream analysis?
R linear-regression residual fitted-values
updated 4.1 years ago by ▴ 220 • written 4.7 years ago by ▴ 160
0
votes
0
replies
1.7k
views
Getting KOBAS species annotation database for salmon (salmo salar)
KOBAS kegg enrichment analysis
4.7 years ago by Michael 56k
0
votes
0
replies
880
views
Advice setting up harware/software for snRNA-seq analysis for a newbie
hardware software single-cell
4.7 years ago by georgytos95 • 0
0
votes
3
replies
2.6k
views
Getting Uniprot accession number
gene RNA-Seq
updated 4.7 years ago by ★ 2.4k • written 5.0 years ago by ▴ 50
1
vote
0
replies
744
views
What is the best approach to correlate expression levels, mutated genes and clinical variables
RNA-Seq correlation mutation
4.7 years ago by Lila M ★ 1.3k
3
votes
6
replies
3.0k
views
low assignment reads % in RNA-seq
rna-seq R
4.7 years ago by parinv ▴ 80
0
votes
0
replies
696
views
Why could I be having only NAs for p_val and p_val_adj in Seurat DGE analysis?
RNA-Seq R rna-seq next-gen gene
4.7 years ago by charlesgwellem ▴ 10
122,213 results • Page 707 of 2445
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Recent Replies
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 ▴ 130
@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.
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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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I don't believe merqury ignores softmasked (lower case) nucleotides so I don't think that is the case. From what it sounds like, during th…
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Thanks a lot to be helpful I’m trying to build a complete `UniProtID` to `GeneSymbol` lookup table and I’m running into a wall. I’ve alrea…
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by thomas.heigl.ibk ▴ 20
thanks for the quick reply. i posted the screenshot. gatk-internally, there is still the difference using -ERC or not, priot is getting …
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by thomas.heigl.ibk ▴ 20
here the igv view. showing the histogram for all samples plus the reads for one: ![enter image description here][1] and expanded view of …
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Arup Ghosh 3.5k
Check the read lengths to make sure the files are correct.
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by Pierre Lindenbaum 166k
> Any suggestions or help you could share please, show us an IGV screenshot of the position GATK realign the reads locally, discards read…
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