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121,962 results • Page 197 of 2440
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1
vote
3
replies
1.2k
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Interpreting the CpG pearson correlation plot
Differential-methylation
24 months ago by bioinfo_ga ▴ 70
0
votes
3
replies
1.3k
views
How do I use fastqc to quality control the third generation sequencing data and establish a reference quality control result?
fastqc
23 months ago by guoxingpeng0904 • 0
3
votes
5
replies
1.7k
views
Access to fastq files on SRA Run browser
NCBI FASTQ SRA
updated 24 months ago by 89k • written 24 months ago by ▴ 10
2
votes
2
replies
915
views
Bar plot in R
R Barplot
updated 24 months ago by 45k • written 24 months ago by ▴ 10
0
votes
2
replies
1.2k
views
HiFi read alignment with vg giraffe
vg
updated 24 months ago by ▴ 760 • written 24 months ago by • 0
0
votes
1
reply
828
views
fasttree running problem
fasttree
updated 24 months ago by 45k • written 24 months ago by • 0
0
votes
0
replies
579
views
What should I do with STAR two-pass novel splice junctions?
RNA-seq
24 months ago by CTLong ▴ 140
0
votes
1
reply
1.8k
views
News: FINAL CALL - Workshop - Single-Cell RNA-Seq Data Analysis: A Practical Introduction (November 8-10, 2023 in Berlin)
workshop RNA-Seq scRNA-Seq single-cell
24 months ago by David Langenberger 11k
3
votes
5
replies
3.3k
views
DSSP: P secondary structure
secondary-structure protein DSSP
updated 24 months ago by 45k • written 3.9 years ago by ▴ 20
1
vote
2
replies
1.4k
views
Is it possible to find the target bed file for TSO500 panel?
bed illumina target
updated 24 months ago by • 0 • written 2.1 years ago by • 0
0
votes
4
replies
1.1k
views
Epigenetic factor associated gene serach
gene-set epigenetics
updated 24 months ago by 45k • written 24 months ago by ▴ 30
0
votes
3
replies
1.2k
views
Missing BUSCOs are actually present in the transcriptome based on BLASTx?
transcriptome blastx BUSCO missing busco
24 months ago by lorenz • 0
0
votes
3
replies
1.2k
views
CPTAC data download
R CPTAC
updated 24 months ago by 45k • written 24 months ago by ▴ 180
0
votes
0
replies
493
views
Collecting a set of random taxonomy IDs
NCBI API taxonomy database
24 months ago by gabrielpenun • 0
0
votes
0
replies
482
views
CAMI dataset source genomes
CAMI metagenome
updated 24 months ago by 45k • written 24 months ago by • 0
0
votes
5
replies
1.2k
views
2 dimensional quadrant plot
2dplot seurat
updated 24 months ago by ★ 19k • written 24 months ago by • 0
0
votes
2
replies
1.1k
views
ROSE superenhancer labels
ROSE ChIP-Seq
updated 24 months ago by 45k • written 2.5 years ago by ▴ 10
1
vote
1
reply
607
views
ROSE Algorithm: index out of range
ROSE super-enhancer
updated 24 months ago by 45k • written 24 months ago by • 0
0
votes
4
replies
1.5k
views
Can not generate tranches plot after VQSR
VariantRecalibrator variant-calling vqsr gatk
updated 24 months ago by 45k • written 2.6 years ago by • 0
0
votes
1
reply
712
views
gene splitted into two contigs
vfdb abricate
updated 24 months ago by ▴ 80 • written 24 months ago by • 0
1
vote
8
replies
2.1k
views
How does one access TCGA controlled data in AWS S3?
tcga aws
updated 23 months ago by ★ 1.3k • written 24 months ago by ▴ 10
1
vote
7
replies
2.0k
views
Ribosomal cluster
seurat single-cell
24 months ago by Chris ▴ 360
0
votes
1
reply
1.1k
views
Changing LFC font size on Complex Heatmap
R complexheatmap deseq2
updated 24 months ago by ★ 3.1k • written 24 months ago by • 0
1
vote
2
replies
955
views
Bacterial RNA-seq GC%
GC-content RNA-seq Bacterial
24 months ago by fluentin44 ▴ 20
0
votes
2
replies
3.9k
views
Removing constant/zero columns for PCA?
R pca
updated 24 months ago by ★ 30k • written 24 months ago by ▴ 160
2
votes
1
reply
1.0k
views
Using sequence percent similarity from alignments to compare duplication events
gene-duplication sequence-alignment
updated 24 months ago by ★ 1.8k • written 24 months ago by ▴ 40
43
votes
44
replies
15k
views
14 follow
Macbook M1 pro/M2 pro or Dell (with Ubuntu/other linux distribution) for bioinformatics stuff?
metagenomics amplicon macbook Intel MacOs
updated 23 months ago by ★ 3.5k • written 2.0 years ago by ▴ 20
0
votes
1
reply
1.3k
views
ROSE Algorithm: list index out of range
ROSE Super-Enhancer
updated 24 months ago by 45k • written 2.1 years ago by • 0
0
votes
2
replies
667
views
Retrieve certain gene from different WGS from NCBI
NCBI WGS
updated 24 months ago by 45k • written 24 months ago by ▴ 10
1
vote
1
reply
765
views
Cancer drug target identification from gene expression data of patients?
cancer gene target
updated 24 months ago by 5.1k • written 24 months ago by ▴ 50
0
votes
1
reply
767
views
Unknown error using MAFToGVCF Plugin from practical haplotype graph (phg) and tassel5
phg
updated 24 months ago by ▴ 420 • written 24 months ago by • 0
0
votes
2
replies
1.0k
views
Diamond blast running in a loop
nanopore blast diamond
24 months ago by bioinfo_ga ▴ 70
0
votes
1
reply
552
views
MSA on clustal
clustal
updated 24 months ago by 45k • written 24 months ago by • 0
0
votes
0
replies
489
views
SeqSQC can be used for sample QC of Whole Genome Sequencing Data
SeqSQC WGS
24 months ago by ttom ▴ 230
2
votes
3
replies
1.3k
views
How to subset dds object properly comparing two conditions
R DESeq2 bioconductor
updated 24 months ago by 45k • written 24 months ago by • 0
0
votes
0
replies
455
views
ggplot layout and figure limits
ggplot2
updated 24 months ago by 45k • written 24 months ago by • 0
1
vote
3
replies
1.4k
views
Multiple alignment of genome assemblies to generate a tree
genome-assemblies multiple-sequence-alignment
24 months ago by pramach1 ▴ 40
2
votes
7
replies
2.6k
views
Finding the Homologous sequences
HMMER Homology
23 months ago by siu ▴ 160
0
votes
0
replies
486
views
Code for implementation of Network Component Analysis
matlab nca python network-component-analysis
updated 24 months ago by 45k • written 24 months ago by • 0
1
vote
1
reply
945
views
Am I correctly running psiblast (using a PSSM as query)?
PSIBLAST PSI-BLAST BLAST
updated 24 months ago by ★ 30k • written 24 months ago by • 0
0
votes
0
replies
943
views
Forum: Steps after doublet detection in single cell data
scRNA doublet
24 months ago by ishwarvh • 0
0
votes
0
replies
479
views
Normalizing Chip seq data using fruit fly genome
normalization humangenome chipseq
24 months ago by Mehvi khan • 0
0
votes
0
replies
502
views
ERROR::INVALID_ALIGNMENT_START Alignment start should be 0 because reference name = *.
Pysam ValidateSamFile
24 months ago by ManuelDB ▴ 110
1
vote
5
replies
2.0k
views
VCF indexing
vcf
updated 24 months ago by 45k • written 24 months ago by • 0
0
votes
9
replies
2.1k
views
multiple protein sequence similarity tool
protein-sequence
updated 24 months ago by 22k • written 24 months ago by • 0
0
votes
0
replies
422
views
Allele-specific expression from bulk tumor RNAseq
RNA-seq ASE
updated 24 months ago by 45k • written 24 months ago by ▴ 20
3
votes
3
replies
1.2k
views
How do mRNASeq, BulkRNASeq, and TotalRNASeq differ in terms of workflow?
RNA-Seq
updated 24 months ago by 45k • written 24 months ago by • 0
1
vote
5
replies
1.5k
views
how to make estimated proteome from genome?
proteome genome
24 months ago by dec986 ▴ 380
1
vote
3
replies
1.2k
views
Download files from EBI ftp
ftp
updated 24 months ago by 89k • written 24 months ago by ▴ 70
1
vote
3
replies
1.2k
views
How to deal with reads which CIGAR is [0-9]+S
CIGAR ampliconclip
updated 24 months ago by ★ 1.4k • written 24 months ago by ▴ 110
121,962 results • Page 197 of 2440
Recent Votes
A: Which is the proper RNA-seq count table transformation to perform hierarchial cl
Answer: Differences between published differential gene expression results and own analy
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Answer: If TPM is not comparable across cohorts, can it be used as the input for ML mode
Answer: Tools to simulate Illumina short read sequences and ONT long reads with a refere
sra-explorer : find SRA and FastQ download URLs in a couple of clicks
Comment: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
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Recent Replies
Comment: Errors with RSEM/bowtie2 by Olivia • 0
I am not sure what you mean by this, but I believe that is what I did. With Trinity, I matched all the paired reads together, so they shoul…
Answer: Gene expression equivalent of polygenic risk score ? by GouthamAtla 12k
I don't think something exists out of the box. With variants, we have a 'weight' for each variant on disease risk (obtained through large s…
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write.table(df1, "df1.txt", sep = "\t", row.names = T, col.names = T, quote = FALSE)
Comment: Errors with RSEM/bowtie2 by GenoMax 154k
That is good confirmation. Bacl to the error message. > I don't know how to fix this, given that I already did the trimming steps. DId yo…
Comment: Differences between published differential gene expression results and own analy by dsull ★ 7.7k
Honestly, those things shouldn't result in a considerable discrepancy. The largest difference will come from the post-processing & analysi…
Answer: Differences between published differential gene expression results and own analy by Ales ▴ 50
I second the comment about comparing the top 100 genes - if you see vastly different results, I would lean closer to examining protocols th…
Answer: Help interpreting BLASTn results and phylogenetic tree for genetics practical by Mensur Dlakic ★ 30k
I think what you are asking involves too much work for anyone to explain it in granular detail. But who knows, maybe there is a good soul o…
Answer: Differences between published differential gene expression results and own analy by yura.grabovska ▴ 830
When you say vastly different, what do you mean exactly? Does your top 100 up/down not match theirs at all?
Comment: Functional prediction for proteins of bacteria. by colindaven 8.0k
Have a look at tools like SnpEff or Ensembl VEP. Perhaps your bacterial sp is included.
Comment: Errors with RSEM/bowtie2 by Olivia • 0
Yes, I already made the transcriptome with these tools, and the CD-HIT-EST fasta file is the transcript file that I am using for RSEM. Then…
Comment: sra-explorer : find SRA and FastQ download URLs in a couple of clicks by Guilherme • 0
Oh, ok. It seems like NCBI stores the files in SRA format (thus needing conversion and database lookups by sra toolkit tools) and EBI store…
Comment: help with modkit on nanopore sequencing data. by andres.firrincieli 3.9k
On the DMR tutorial page, they retrieve Human CpG Islands from the UCSC Table Browser. You can do the same thing for Mouse CpG Islands. Hav…
Comment: After doublet detection in 10x scRNA-Seq data, there is still evidence of double by yura.grabovska ▴ 830
Yes but the problem is that biological knowledge is never fully encompasing. While I can say that a cell expressing CD45 alongside astrocyt…
Comment: DNA copy number blacklist for excluding common unreliable regions by yura.grabovska ▴ 830
Human genome, ideally hg38
Comment: Is Newbler still available for download by anweshaash • 0
Hello, I am wondering if you got access to the software or not. I am looking to use Newbler for my research and I contacted Roche too but t…
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