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121,434 results • Page 921 of 2429
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5
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5
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2.9k
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What Regulates Alternative Splicing And Intergenic Trans Splicing?
splicing
updated 5.2 years ago by ▴ 20 • written 12.1 years ago by ▴ 10
2
votes
3
replies
1.7k
views
How to get Gene ID from NCBI accession for non model species ?
gene id ncbi accession
updated 5.2 years ago by 152k • written 5.2 years ago by ▴ 680
0
votes
11
replies
4.0k
views
How to extract a specific gene sequence from a batch of genome files that I have?
genome gene sequence alignment
5.2 years ago by drdrnaveenkumar • 0
3
votes
2
replies
4.9k
views
Cellranger on mac?
RNA-Seq alignment
updated 5.2 years ago by 88k • written 5.2 years ago by ▴ 10
12
votes
12
replies
2.1k
views
7 follow
Forum: Who qualify as a world class bioinformatician as seen in job ads
world-class bioinformatician qualification
updated 2.0 years ago by 45k • written 5.2 years ago by • 0
0
votes
0
replies
794
views
know sites of rice for BaseRecalibrator
DNA-SEQ
5.2 years ago by 543541656 ▴ 20
0
votes
12
replies
5.8k
views
Differential expression testing in Seurat
RNA-Seq seurat R
updated 3.5 years ago by 88k • written 5.2 years ago by ▴ 70
0
votes
3
replies
1.1k
views
Need help finding data from Google's DeepVariant paper
genome snp sequencing
updated 5.2 years ago by 20 • written 5.4 years ago by ▴ 80
0
votes
0
replies
586
views
Using RNA-seq to measure SCU
RNA-Seq Synonymous codon usage mapping
5.2 years ago by 2405592M ▴ 160
4
votes
7
replies
1.6k
views
blast error ?creating index
blast index database genome fasta
5.2 years ago by alhafidzhamdan • 0
0
votes
1
reply
1.4k
views
Saturation analysis of chip-seq peaks
ChIP-Seq R
5.2 years ago by alhafidzhamdan • 0
0
votes
0
replies
665
views
Stuck at equilibration step6.1
namd2 molecular dynamics charmm gui hmmm
updated 5.2 years ago by 152k • written 5.2 years ago by • 0
2
votes
4
replies
1.6k
views
Problem with ks_debruijn4 on large dataset in KisSplice
RNA-Seq software error kissplice
updated 5.2 years ago by ▴ 150 • written 5.7 years ago by ▴ 10
5
votes
4
replies
1.4k
views
DNA-Seq and Whole Genome Sequencing, are they the same?
genome dna-seq whole genome sequencing
updated 5.2 years ago by 88k • written 5.2 years ago by ▴ 30
2
votes
6
replies
1.5k
views
Problems in Variant Calling Code
SNP Variant Calling
5.2 years ago by arjun.murthy779 ▴ 10
2
votes
5
replies
5.2k
views
Filtering the genes based on cpm in edgeR
RNA-Seq edgeR
5.2 years ago by elb ▴ 260
0
votes
0
replies
378
views
Use of MYGene.py with previous build version
RNA-Seq
5.2 years ago by auesro • 0
0
votes
0
replies
808
views
is the output.table correct after BQSR?
gatk bqsr
updated 5.2 years ago by 166k • written 5.2 years ago by ▴ 20
0
votes
0
replies
573
views
How to sort the TCGA dataset based on expression of a panel of genes?
RNA-Seq
5.2 years ago by dr.goutham • 0
0
votes
0
replies
1.3k
views
RNA log2 fold change in FPKM
RNA-Seq
5.2 years ago by 9521ljh ▴ 50
0
votes
1
reply
784
views
What can you do with whole genome sequecing by illumina of a crop population
next-gen sequencing genome
5.2 years ago by Hann ▴ 120
0
votes
2
replies
2.9k
views
Split bam into chunks but keep reads mapped to the same region together
alignment BAM split
updated 5.2 years ago by ★ 2.9k • written 5.2 years ago by • 0
0
votes
7
replies
2.1k
views
What's the best way to serve VCF data on web?
vcf web database postgres
updated 5.2 years ago by ★ 2.9k • written 5.2 years ago by ▴ 30
1
vote
4
replies
667
views
"C" and "G" positions
R genome
5.2 years ago by denafridman • 0
1
vote
4
replies
1.2k
views
Extract SV indicating pair-end reads
Structure Variation pair-end sequencing
updated 5.2 years ago by ★ 2.9k • written 5.3 years ago by • 0
12
votes
7
replies
9.3k
views
Using Ruby To Convert Csv File To Fasta
fasta
updated 5.2 years ago by 20 • written 13.8 years ago by ▴ 170
1
vote
6
replies
2.9k
views
fusion detection for DNA Sequencing data
fusion NGS DNA
updated 9 months ago by ▴ 270 • written 5.2 years ago by ▴ 930
0
votes
0
replies
548
views
SNP Feature File
SNP Bacterium
5.2 years ago by arjun.murthy779 ▴ 10
0
votes
0
replies
809
views
Can I use VarScan2 CNV using non normal-tumor pair?
cnv varscan2
5.2 years ago by ruddae43 • 0
0
votes
1
reply
864
views
Pathway targeted genes
Pathway
updated 5.2 years ago by ▴ 200 • written 5.2 years ago by ▴ 310
1
vote
4
replies
2.4k
views
there is an error after samtools index
DNA-SEQ
updated 5.2 years ago by 15k • written 5.2 years ago by ▴ 20
0
votes
2
replies
831
views
Issue separating mate pair fastq files from a paired-end sequencing dataset
next-gen rna-seq RNA-Seq sequencing fastq
5.2 years ago by marvel479 • 0
0
votes
4
replies
1.3k
views
R circlize package problem with drawing histogram
R genome circlize Rcirc Circos
5.2 years ago by marvel479 • 0
4
votes
0
replies
2.2k
views
Tutorial: NIH CDE browser for TCGA clinical data CDE codes
nih tcga metadata cde
updated 2.3 years ago by 45k • written 5.2 years ago by 89k
4
votes
7
replies
2.2k
views
How many samples are good to find significant targets using GISTIC?
gene
5.2 years ago by joyk2a ▴ 30
1
vote
1
reply
1.1k
views
Python script for sequence alignment not running
python alignment
updated 5.2 years ago by ★ 29k • written 5.2 years ago by ▴ 30
2
votes
2
replies
3.5k
views
PLINK - Sample(s) present with no genotype data
plink
updated 5.2 years ago by 11k • written 5.2 years ago by ★ 1.5k
2
votes
4
replies
2.9k
views
Why is hmmsearch only using the 1st HMM in a concatenated HMM database?
hmm hmmer protein domain bash script
updated 5.2 years ago by ★ 29k • written 5.2 years ago by ▴ 740
2
votes
2
replies
4.8k
views
SNP subsetting using bcftools
SNP next-gen bcftools
updated 5.2 years ago by 89k • written 5.2 years ago by ▴ 10
0
votes
1
reply
1.4k
views
GSEA/fold change for ChIP-seq
ChIP-Seq
5.2 years ago by yepeh72919 ▴ 10
8
votes
2
replies
2.9k
views
Python script to find ORFs not returning expected results for final frame
sequence Python ORF
updated 5.2 years ago by 20 • written 9.0 years ago by ▴ 40
1
vote
2
replies
2.2k
views
Getting a GTF of expressed repeat annotation from Ensembl
RNA-Seq sequence
5.2 years ago by akh22 ▴ 120
0
votes
0
replies
784
views
Interpreting Orthofinder and erminej results?
genome assembly gene sequence Assembly
5.2 years ago by bobyjoe07 • 0
1
vote
4
replies
3.3k
views
GISTIC results. Too many deleted genes?
gistic cnv SNP
updated 5.2 years ago by 89k • written 6.7 years ago by ▴ 40
3
votes
2
replies
5.2k
views
The outputs of GISTIC
GISTIC CNV Copy number
updated 5.2 years ago by 89k • written 9.0 years ago by ▴ 200
2
votes
0
replies
954
views
News: Landscape Genomics course ONLINE
snp R next-gen
updated 2.0 years ago by 45k • written 5.2 years ago by ★ 2.6k
0
votes
0
replies
560
views
Relationship between instantaneous rate of change and global clock model?
clock model markov chain rate of change
5.2 years ago by Namenlos • 0
1
vote
3
replies
3.5k
views
single cell RNA seq Differential Expression using MAST
rna-seq RNA-Seq next-gen sequencing
updated 5.2 years ago by 88k • written 5.2 years ago by • 0
2
votes
7
replies
2.0k
views
GridION fastq ASSEMBLY
Nanopore Assembly fastq
5.2 years ago by shira.zaltsman ▴ 20
0
votes
0
replies
793
views
Reference Background for TF Motif Enrichment Analysis
ChIP-Seq
5.2 years ago by dalia.halawani12 • 0
121,434 results • Page 921 of 2429
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Answer: Beagle PATH (partially) recognised on Ubuntu 22.04
How to do a local denovo assembly including unmapped paired reads for many samples to genotype a large insertion.
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Answer: Pharokka Error
Answer: Should I perform integration to correct batch effects?
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Recent Replies
Comment: DESeq2 design for differential expression with 2 timepoints and 2 controls by jkim ▴ 190
Have a look at [the contrast and interaction section](https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#in…
Answer: Beagle PATH (partially) recognised on Ubuntu 22.04 by GenoMax 152k
> I can run BEAST only in the same terminal window if I have have executed the export PATH command first. If I open a new terminal and try …
Answer: custom BED to UCSC genome browser by Maximilian Haeussler ★ 1.7k
Hi, we just added bedMethyl support! Try it at https://genome-test.gi.ucsc.edu/cgi-bin/hgTables. type must be "bedMethyl". Please let us kn…
Answer: custom BED to UCSC genome browser by barslmn ★ 2.4k
BED files have specific format. https://genome.ucsc.edu/FAQ/FAQformat.html#format1 UCSC uses these columns to display the tracks. Your fil…
Comment: Should I perform integration to correct batch effects? by han ▴ 30
Thank you very much for your detailed and thoughtful response! It was very helpful and clarified several important points regarding integra…
Comment: identify unmapped regions by María José ▴ 10
We've been analyzing chromosome coverage files for our samples and have encountered some significant gaps with no coverage at all. To inves…
Comment: Is this the correct DESeq2 design for model with interaction terms and batch eff by ATpoint 88k
Yes, batch and donor are usually not compatible, do one or the other. Donor (so paired analysis) is imo always preferred as most powerful, …
Comment: Host Removal Issues Human/Dog with samples containing Eukaryotic species by Mensur Dlakic ★ 29k
Binning doesn't separate any particular organisms. It separates DNA contigs based on tetranucleotide frequencies. Eukaryotes use different …
Comment: Host Removal Issues Human/Dog with samples containing Eukaryotic species by Jon • 0
I can't argue with you, I'm just having problems wrapping my brain around the issue. I have wondered if the reference that NCBI BLAST is …
Comment: SE reads in fr-firststrand, fr-secondstrand by JourneyToAbyss ▴ 250
Not trying to dig up a old thread. However, I believe Antonio is incorrect. [this](https://academic.oup.com/bfg/article/19/5-6/339/5837822?…
Comment: Host Removal Issues Human/Dog with samples containing Eukaryotic species by Jon • 0
Yes, the samples were collected correctly aseptically, via nurse with correct methodology. Subject 1 there are 4 different samples (shotgu…
Answer: Host Removal Issues Human/Dog with samples containing Eukaryotic species by Mensur Dlakic ★ 29k
It is impossible that *N. fowleri* has high identity to humans, or else it would be classified as a primate rather than an amoeba. Even org…
Comment: Host Removal Issues Human/Dog with samples containing Eukaryotic species by GenoMax 152k
If possible I suggest that you find someone who can easily access your entire dataset locally and would be willing to help out.
Comment: Host Removal Issues Human/Dog with samples containing Eukaryotic species by GenoMax 152k
> Naegleri Fowleri Karachi NF001, which is the one identified by BLAST BLAST should only be used for qualitative purposes for NGS data. >…
Comment: Host Removal Issues Human/Dog with samples containing Eukaryotic species by Jon • 0
If you're interested enough to look at the read files yourself, I would be happy to provide them. I keep running into things that I just …
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