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Filtering for tag: Sequencing • reset
0
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21
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Why GC content is important on NIPT results?
NGS NIPT Sequencing
updated 1 hour ago by ★ 2.0k • written 2 hours ago by • 0
0
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0
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27
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Minimum enrichment score to take for analysis
Sequencing Rna-Seq
1 day ago by ashwing.kofficial • 0
4
votes
6
replies
3.5k
views
Fastqc shows over-represented sequence with no sequence given?
sequencing
updated 1 day ago by • 0 • written 5.8 years ago by ▴ 50
0
votes
0
replies
45
views
Samtools vcf file filtering
samtools RNAseq sequencing
4 days ago by bandanaschapagain ▴ 30
0
votes
2
replies
112
views
How to use deseq 2 file for keggscape in cytoscape
RNA-SEQ Visualization Sequencing Cytoscape
3 days ago by ashwing.kofficial • 0
0
votes
4
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170
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extract unmapped reads from WGS data - which samtools parameters to choose
WGS Sequencing
updated 4 days ago by ▴ 170 • written 5 days ago by ▴ 20
2
votes
4
replies
251
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What are the disadvantages of increasing the sequencing depth of RNA-seq experiment?
NGS RNA-Seq sequencing depth transcriptome
10 days ago by mrj ▴ 20
0
votes
2
replies
92
views
Power analysis to determine sample size for a single-cell sequencing study
sequencing single-cell
11 days ago by halo22 ▴ 250
0
votes
0
replies
64
views
Troubleshooting abnormal ATAC-seq diagnostic plots
QC Sequencing ATAC-seq Troubleshooting
11 days ago by cwwong13 • 0
3
votes
3
replies
164
views
Can I pool RNA-seq library with ATAC-seq library and sequence in the same S4 lane?
RNA-seq Sequencing ATAC-seq
updated 11 days ago by 99k • written 11 days ago by • 0
0
votes
0
replies
80
views
How important is aligning BAM files to the appropriate design file?
gatk sequencing genomics wes bam
12 days ago by jon.klonowski ▴ 70
1
vote
5
replies
247
views
What is the most accurate short (ish) read aligner?
aligner sequencing bwa minimap2
updated 10 days ago by 87k • written 12 days ago by ▴ 90
0
votes
1
reply
85
views
MSI cslculation
bed sequencing annotation
updated 12 days ago by ★ 2.0k • written 12 days ago by • 0
6
votes
5
replies
259
views
Comparison of samples to find the best parameters for RNA-seq
NGS rna fastq R sequencing
updated 12 days ago by 87k • written 13 days ago by • 0
0
votes
7
replies
330
views
Another infer_experiment.py interpretation question
RNA-Seq sequencing
updated 11 days ago by ★ 1.4k • written 3 months ago by • 0
0
votes
2
replies
188
views
RSEM Calculate Expression Error
rsem frequency coding RSEM sequencing
12 days ago by mh9236183 • 0
0
votes
0
replies
112
views
Does GATK4 provide better quality of SNP/Indels calls over GATK3.8?
sequencing
updated 13 days ago by 72k • written 13 days ago by • 0
1
vote
2
replies
869
views
single cell sequencing data doublets removal tools selection
sequencing
updated 13 days ago by ★ 1.6k • written 22 months ago by ▴ 330
0
votes
0
replies
130
views
Job: Postdoctoral fellowship in Bioinformatics in Houston
RNAbiology python sequencing bioinformatics
13 days ago by chunlei.yu1990 • 0
1
vote
1
reply
108
views
Forum: Sharing frequently asked questions about microbial genome sequencing II
microbial faq genome sequencing meta
updated 13 days ago by 87k • written 14 days ago by ▴ 100
2
votes
2
replies
191
views
How to find that genes are up or down-regulated in which condition
enrichment sequencing python genomics
14 days ago by StartR ▴ 20
0
votes
1
reply
113
views
bcftools csq creates no output
genotyping sequencing dna format
15 days ago by ommegang ▴ 10
2
votes
1
reply
158
views
BWA-MEM or BWA-ALN + BWA-SAMSE for MGI sequencing
bwa ali sequencing
updated 15 days ago by 47k • written 15 days ago by • 0
3
votes
4
replies
308
views
Alignment Viewer
sequencing alignment
updated 13 days ago by 99k • written 15 days ago by ▴ 30
3
votes
17
replies
785
views
FAIRE for non-standard cultivar, mapping to reference, MAPQ
sequencing faire mapping
10 days ago by boczniak767 ▴ 740
0
votes
1
reply
2.0k
views
Regarding valid transcript and Transdecoder output
sequencing Transdecoder transcript assembly
updated 15 days ago by ▴ 170 • written 4.9 years ago by ★ 1.5k
2
votes
1
reply
253
views
Using Seurat to take in a Normalised TPM Gene to Cell matrix as a Seurat Object
format sequencing rna
updated 17 days ago by 9.2k • written 17 days ago by • 0
0
votes
0
replies
108
views
Job: Postdoc openings @ NYC: Epigenetics / Long Reads / Microbiome
sequencing RNAseq microbiome methylation
9 days ago by fanggang ▴ 100
0
votes
0
replies
72
views
DNAzymes
sequencing
17 days ago by maryamtashakori96 • 0
3
votes
4
replies
279
views
SARS-Cov-2 variant calling
sequencing variants sars-cov-2
updated 17 days ago by 87k • written 17 days ago by ▴ 90
0
votes
11
replies
658
views
bbmap for FAIRE-seq and other line than reference
aligner mapping sequencing
15 days ago by boczniak767 ▴ 740
0
votes
1
reply
165
views
alternative splicing analysis
aligner rna-seq sequencing rna pipeline
updated 18 days ago by ▴ 140 • written 19 days ago by • 0
1
vote
4
replies
260
views
is it possible to extract all the exome information from WGS?
genome sequencing
updated 18 days ago by 48k • written 18 days ago by ▴ 50
0
votes
0
replies
84
views
Single end or paired end LP WGS
alignment mapping sequencing genomics
19 days ago by am ▴ 20
1
vote
0
replies
88
views
Forum: Sharing frequently asked questions about microbial genome sequencing (Part 1)
sequencing faq BI microbial genome
20 days ago by guoxuantong ▴ 100
0
votes
0
replies
101
views
Identify cell type from bulk RNA sequencing data
sequencing type clustering r
20 days ago by minoo • 0
5
votes
3
replies
551
views
What Machine Learning, AI, Deep Learning, & Neural Network Python packages do you use in Bioinformatics and/or whole genome sequencing annotation?
data python sequencing
updated 19 days ago by 9.2k • written 20 days ago by ▴ 20
1
vote
0
replies
90
views
Empty result obtained when using SAMTOOLS and MPILEUP to generate consensus sequences FASTQ file
sequencing fasta fast dna
20 days ago by roelofco ▴ 10
0
votes
0
replies
82
views
Differential methylation analysis and correlation to gene expression
genomics rna dna sequencing
21 days ago by deenfortune • 0
0
votes
2
replies
236
views
Concatenating fastq files for better assembly
genomics assembly sequencing RNA-Seq
19 days ago by shail.nair05 ▴ 10
0
votes
0
replies
757
views
Job: 2 Computational Biologist / Data scientist positions in single-cell and multi-OMICs data integration at Institut Imagine (Paris, FR)
genomics bioinformatics single-cell sequencing job
20 days ago by fracarb8 ▴ 130
7
votes
6
replies
377
views
What do these MA plots signify?
seq rna maplot sequencing deseq2
updated 18 days ago by ▴ 90 • written 21 days ago by ▴ 10
0
votes
4
replies
190
views
How to quickly find the position of k-mer on the genome
alignment sequencing k-mer
updated 22 days ago by ▴ 30 • written 4 weeks ago by • 0
1
vote
2
replies
188
views
How to get raw read counts of genes/cds/transcripts from SAM/BAM file?
RNA-Seq alignment gene sequencing assembly
22 days ago by shail.nair05 ▴ 10
1
vote
2
replies
102
views
Want to know whether this p-adj value is acceptable
RNA-Seq next-gen sequencing
updated 23 days ago by 47k • written 23 days ago by • 0
0
votes
5
replies
415
views
I am scaffolding using HiC data and found many contigs are out of the chromosome. Please help me.
sequencing assembly
updated 21 days ago by 48k • written 23 days ago by • 0
0
votes
2
replies
176
views
How to make paired-end sequencing multi-mapping reads have only the optimal two reads
RNA-Seq alignment sequencing
19 days ago by minghuiguo448 • 0
0
votes
1
reply
171
views
Deletions together with SNVs on BAM files
alignment sequencing genome browser
23 days ago by baliczap • 0
0
votes
0
replies
179
views
Looking to annotate concatenated VCF files on Galaxy for Hg19 reference genome. Need setup guidance.
genome next-gen sequencing sequence gene
updated 24 days ago by 20 • written 9 weeks ago by ▴ 20
0
votes
0
replies
150
views
Job: Bioinformatics Curator Positions with Computercraft @ NCBI
job sequencing bioinformatics Job
24 days ago by jyu ▴ 40
6,095 results • Page 1 of 122
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Recent Replies
Answer: Is it possible to annotate a file for the human genome using the command line wi by GenoMax 99k
As shown in the [**README**][1], `provean` should run on the command line. [Download][2] and follow install directions. This program requir…
Comment: correlation analysis of a single variable versus multiple variables by ATpoint 47k
> My results will be strong enough for a publication? If you plan to publish a few correlation tables for a single gene then the answer is…
Comment: Converting Braker2 gtf output to gff then genbank by robert.murphy ▴ 40
Oh it is simply whether the DNA is circular or linear, I thought it was something more complicated like chromatin organisation! Thank you.
Comment: Does GISAID fasta files contain spike protein or whole genome sequence? by Devon Ryan 98k
Why not look at the file and find out? You have the sequences, figure it out.
Comment: Converting Braker2 gtf output to gff then genbank by Juke34 ★ 5.3k
You can get some information calling the EMBLmyGFF3 adanced help: ``` EMBLmyGFF3 --advanced_help topology ``` Otherwise you can find verbo…
Comment: Converting Braker2 gtf output to gff then genbank by robert.murphy ▴ 40
In `EMBLmyGFF3` script should I concern myself much with the `topology` option? If yes do you have suggestions for good places to educate (…
Comment: Why GC content is important on NIPT results? by German.M.Demidov ★ 2.0k
NIIPT can be performed in various variations and for different purposes. Is it chromosome abnormalities test in your case? If so, extreme G…
Comment: bedops wig2bed 'Row begins with a tab or space' error by a_bis • 0
The output looks as follows: 1^I0^I3000060^I0.000000$ 1^I3000060^I3000090^I0.224911$ 1^I3000090^I3000120^I0.449820$ 1^I30…
Comment: Samtools view filter by reference sequence by maxrwjones898 • 0
Thanks for your answer, I will give this a go!
Answer: Variant calling from comparison of assembled genomes where there is only one r by Hans ▴ 120
It appears that bcftools takes into consideration the alignments of all genotypes when it calls variants. When I call the variants separat…
Comment: What Coverage allele-fraction threshold to use? by German.M.Demidov ★ 2.0k
At each genomic position you have a specific coverage, say X. Y out of X reads may support an alternative variant, X - Y - reference. You n…
Answer: Finding all instances of a recurring motif in a repeat protein by Mensur Dlakic ★ 10k
Some papers to consider: - https://academic.oup.com/bioinformatics/article/24/6/807/194276 - https://academic.oup.com/bib/article/15/…
Comment: why my volcano plot looks strange? by ATpoint 47k
First thing to do would be to not use custom statistics but a proper framework such as limma. There are quite some peptides (or whatever yo…
Answer: Help with CNV calling using ExomeDepth by Joakim ▴ 10
Instead of using bedframes from data(genes.hg19) and data(exons.hg19) in ExomeDepth, I got them from the UCSC Table Browser for hg38 (http:…
Answer: How to grep scaffold from the vcf file by Pierre Lindenbaum 135k
bcftools view --regions-file file1.txt input.vcf
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