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1,000 results • Page 3 of 20
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0
votes
9
replies
1.2k
views
Normalization across different single cell RNAseq experimetns
global-scaling single-cell scRNA-seq batch-effect
updated 12 days ago by 43k • written 3.9 years ago by ▴ 20
1
vote
9
replies
892
views
Command line or python RNA-seq read simulator
simulation RNA-seq
5 months ago by i.sudbery 19k
2
votes
9
replies
7.6k
views
6 follow
Read MAP and PED files in PLINK
GWAS PLINK
updated 4 months ago by 141k • written 6.0 years ago by • 0
0
votes
9
replies
2.4k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome nanopore basecalling fastq
updated 8 hours ago by • 0 • written 8 months ago by • 0
1
vote
9
replies
627
views
Problem with ONT sequencing pipeline. Probably in the Samtools part
bam samtools ONT
updated 3 months ago by 141k • written 3 months ago by • 0
6
votes
9
replies
2.9k
views
How to analyze the scRNA seq Fastq files from NCBI
SRAtool Cellranger NCBI
updated 10 months ago by 43k • written 2.3 years ago by ▴ 20
1
vote
9
replies
664
views
Htseq-count reads with missing mate encountered
htseq htseq-count
5 months ago by Bjorn • 0
0
votes
9
replies
596
views
99.9999% of Q30 bases is normal?
RNA-seq fastp
updated 17 days ago by 4.2k • written 18 days ago by ▴ 20
1
vote
9
replies
1.2k
views
Trying to edit VCF file
VCF R bcftools snpsaurus
updated 10 months ago by 43k • written 10 months ago by • 0
0
votes
9
replies
912
views
fragments file generation via Sinto from CellRanger output
scATAC alignment scRNA Sinto 10x
6 months ago by ntsopoul ▴ 60
0
votes
9
replies
1.4k
views
Samtools sam to bam error
samtools
updated 6 months ago by • 0 • written 2.0 years ago by ▴ 10
4
votes
9
replies
1.0k
views
bcl2fastq troubleshooting all reads dumped to "Undetermined"
demultiplex illumina sequencing
updated 4 months ago by 141k • written 4 months ago by ▴ 120
0
votes
9
replies
1.7k
views
WCGNA to Cytoscape
wgcna cytoscape rna-seq
updated 12 weeks ago by 43k • written 3.7 years ago by ▴ 40
3
votes
9
replies
793
views
Understanding this analysis pipeline
reads
updated 10 months ago by 43k • written 10 months ago by • 0
1
vote
9
replies
1.5k
views
blast retrieves "N/A" for taxonomic data
blast blastn
updated 7 weeks ago by • 0 • written 3.4 years ago by ▴ 50
2
votes
9
replies
846
views
TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 5 days ago by 4.2k • written 6 months ago by • 0
4
votes
9
replies
580
views
variant calling
variant-calling
updated 25 days ago by 43k • written 26 days ago by • 0
0
votes
9
replies
986
views
gene id
gene-id NCBI
updated 10 months ago by 141k • written 10 months ago by • 0
1
vote
9
replies
532
views
miRNA alignment with Bowtie2
bowtie2
6 weeks ago by Chironex ▴ 40
0
votes
9
replies
1.1k
views
grep multiple lines form file
shell-script grep
updated 10 months ago by 43k • written 4.0 years ago by ▴ 30
0
votes
9
replies
5.4k
views
Calculating FPKM and TPM by hand from htseq-count output?
RNA-Seq rna-seq htseq FPKM TPM
updated 8 months ago by 82k • written 5.0 years ago by ▴ 210
1
vote
9
replies
3.3k
views
build databses for genome using snpEff
annotation SNP snpEff
updated 8 months ago by • 0 • written 5.7 years ago by • 0
1
vote
9
replies
4.4k
views
Unable to install bioconda and bowtie
bioconda conda
updated 4 months ago by 13k • written 19 months ago by ▴ 30
1
vote
9
replies
1.0k
views
gene annotation
gtf gene-annotation
updated 11 months ago by 43k • written 11 months ago by • 0
4
votes
9
replies
2.6k
views
Blast+ remote database names
blast remote databases Blastplus
updated 9 months ago by 141k • written 2.3 years ago by • 0
3
votes
9
replies
976
views
Estimate sizes of repeats in a especific Gene
CGG Fragile-X
11 months ago by Rafael ▴ 10
1
vote
9
replies
620
views
Approach for multi species comparative transcriptomics and differential expression analyses
DE RNA-seq transcriptomics
updated 3 months ago by ★ 1.9k • written 3 months ago by • 0
0
votes
9
replies
781
views
how to use multiple command in one line with using the output of last command to the next
bedtools linux bed
4 months ago by sata72 • 0
0
votes
9
replies
542
views
Low number of both surviving reads after trimming
trimmomatic trimming
4 weeks ago by Jay • 0
0
votes
8
replies
1.3k
views
Creating fastq subsets from existing files
scRNA-seq umi_tools cellranger fastq
8 months ago by Zack • 0
5
votes
8
replies
2.4k
views
SV calling using giraffe/vg
vg Giraffe calling structural variant
updated 9 months ago by ▴ 460 • written 15 months ago by • 0
0
votes
8
replies
9.9k
views
how to find a read by name in a bam file
next-gen-sequencing
updated 10 months ago by 43k • written 6.8 years ago by • 0
4
votes
8
replies
1.9k
views
Hello, I have differential ATAC-seq from control and diseased cells (H3K27ac mark as chromatin mark) and wondering how to call enhancers using ROSE …
super-enhancers Enhancers
updated 12 weeks ago by ★ 16k • written 3 months ago by • 0
3
votes
8
replies
988
views
Single read sequence from a .fasta file cannot be aligned/BLASTN-d to my reference
BLAST bowtie2 BWA alignment
8 months ago by cheesefish21 ▴ 10
0
votes
8
replies
1.5k
views
VCF samtools
vcf samtools variant-calling
updated 10 months ago by 43k • written 2.4 years ago by • 0
4
votes
8
replies
1.8k
views
Error while running nf-core/rnaseq pipeline
nf-core RNA-seq
11 months ago by eesha28112001 • 0
3
votes
8
replies
909
views
Can these RNAseq runs be combined?
transcriptomics replicates RNAseq
updated 10 months ago by 141k • written 10 months ago by • 0
3
votes
8
replies
624
views
Huge decrease of BUS records using bustools
single-cell bustools 10X
8 weeks ago by julien.wollbrett • 0
0
votes
8
replies
5.3k
views
8 follow
cellranger mkref failed
next-gen-sequencing software-error RNA-seq
updated 19 days ago by • 0 • written 4.7 years ago by ▴ 180
0
votes
8
replies
565
views
STAR aligner options
STAR
4 weeks ago by theophile • 0
1
vote
8
replies
1.1k
views
How does one access TCGA controlled data in AWS S3?
tcga aws
updated 6 months ago by ★ 1.2k • written 6 months ago by ▴ 10
4
votes
8
replies
1.2k
views
Error executing nf-core/metaboigniter pipeline
nf-core metaboigniter nextflow
updated 8 months ago by ★ 1.4k • written 8 months ago by • 0
0
votes
8
replies
653
views
Phobius error: Could not read provided fasta sequence at phobius.pl line 408
Phobius
updated 8 weeks ago by ▴ 10 • written 3 months ago by ▴ 30
1
vote
8
replies
1.3k
views
Betacoronavirus.00.nsq error
biostars-handbook corona
updated 10 months ago by 43k • written 2.3 years ago by • 0
4
votes
8
replies
2.0k
views
How to extract promoter sequences from a plant draft genome?
promoter genome
updated 11 months ago by 43k • written 4.6 years ago by ▴ 120
7
votes
8
replies
9.0k
views
Determining read count
trimmomatic rna-seq trinity
updated 8 months ago by 43k • written 8.0 years ago by ▴ 110
2
votes
8
replies
2.9k
views
How to convert a database from protein to nucleotide
blastn unix blastx blast
updated 11 months ago by 43k • written 7.1 years ago by • 0
0
votes
8
replies
1.9k
views
Chromosome Location of Sequence in Fasta File using Biopython
biopython python
updated 10 months ago by 43k • written 4.4 years ago by • 0
1
vote
8
replies
1.1k
views
Mitochondrial genes - TPM calculation bulk RNA-Seq
TPM RNA-Seq mtDNA
5 months ago by nick_b55 ▴ 10
5
votes
8
replies
604
views
Multiple threads on ubuntu server
Ubuntu
updated 3 months ago by 6.4k • written 3 months ago by ▴ 50
1,000 results • Page 3 of 20
Recent Votes
Comment: How many reads for WGS Sequencing?
Comment: How many reads for WGS Sequencing?
Comment: How many reads for WGS Sequencing?
Comment: How many reads for WGS Sequencing?
Comment: NGS forensics: how to know if data is fabricated
Answer: NGS forensics: how to know if data is fabricated
Comment: NGS forensics: how to know if data is fabricated
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Recent Replies
Comment: How many reads for WGS Sequencing? by Ruqaiya • 0
got it! even if i'm doing the assembly for paired end with both the files do i have set the threshold to 1000bp ?
Comment: NGS forensics: how to know if data is fabricated by Philipp Bayer 8.4k
i've been in our org trying to push such a detector, our use-case is much more limited: I want to make simulated eDNA libraries as real as …
Answer: Differential Expression using Isoseq-supplemented reference transcriptome by Gordon Smyth ★ 7.0k
> What is the best method to test for differential abundance at the isoform level? Salmon returns TPM values instead of the counts which Li…
Answer: Finding batch and outlayers by Tigran • 0
![enter image description here][1] [1]: /media/images/aa60b9ef-b08c-4093-9f0d-fb656a5c
Comment: NGS forensics: how to know if data is fabricated by benformatics 3.9k
Can you post an IGV screenshot of what this looks like?
Comment: NGS forensics: how to know if data is fabricated by benformatics 3.9k
Yeah some of the Illumina machines pre-trim adapters (not sure if this is still the standard). I've also definitely also seen quality-trimm…
Comment: PDB related issue by noodle ▴ 540
You can typically find much more useful info in the cif file, for example what you've found is called '_atom_site.pdbx_PDB_ins_code ' and d…
Comment: PDB related issue by Mensur Dlakic ★ 27k
The best way to find out is to read the original paper. My guess is that the residue has been crystallized in alternative conformations, wh…
Answer: NGS forensics: how to know if data is fabricated by Mensur Dlakic ★ 27k
I share the opinion by @philippbayer I have seen enough questionable things in life and in science to keep me permanently jaded, but there…
Comment: How many reads for WGS Sequencing? by Mensur Dlakic ★ 27k
I downloaded the data in two files from the link you provided. With this command: megahit -1 ERR072246_1.fastq.gz -2 ERR072246_2.fastq…
Comment: How many reads for WGS Sequencing? by Mensur Dlakic ★ 27k
If you have Linux the assembly should work on your system, but 8 GB is generally not enough for assembling larger genomes.
Comment: How many reads for WGS Sequencing? by Mensur Dlakic ★ 27k
I think you might be getting stuck on less relevant parts of my exercise. The most important point was that nothing is wrong with the data.…
Comment: What does it mean single base resolution in sequencing? by dsull ★ 5.9k
Great comprehensive explanation and overview of the technologies -- with regards to sequencing assays, the one thing I'd add is SNV identif…
Answer: What does it mean single base resolution in sequencing? by dsull ★ 5.9k
I think that term means slightly different things in different contexts. For example, it's useful to profile mRNA modifications (e.g. m6a) …
Comment: Cannot process all the reads in a fast5 file? by chujie • 0
Hi, I met the same problem, have you found the solution?
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