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1,000 results • Page
3 of 20
Sort: replies
Rank
Views
Votes
Replies
0
votes
9
replies
1.5k
views
Chipseq analysis on repeat genes
galaxy
repeatmasker
ChIP-seq
repeat-elements
ATAC-seq
updated 7 months ago by
rfran010
▴ 900 • written 7 months ago by
pb11
▴ 10
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
911
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
Andrea
• 0 • written 2.0 years ago by
kb_93
▴ 10
1
vote
9
replies
4.4k
views
Unable to install bioconda and bowtie
bioconda
conda
updated 4 months ago by
rpolicastro
13k • written 19 months ago by
n.anuragsharma
▴ 30
4
votes
9
replies
1.0k
views
bcl2fastq troubleshooting all reads dumped to "Undetermined"
demultiplex
illumina
sequencing
updated 4 months ago by
GenoMax
141k • written 4 months ago by
MaxF
▴ 120
1
vote
9
replies
870
views
Python3 or Ubuntu, not perl: Have Primers with Degenerate Bases, Need tool or way to List all Possible Nucleotide Sequences
degenerate-bases
python
primers
biopython
updated 6 weeks ago by
Dave Carlson
★ 1.7k • written 6 weeks ago by
Matthew
• 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
Ram
43k • written 2.3 years ago by
aimanbarki
▴ 20
3
votes
9
replies
1.7k
views
How to get negative training set if I don't know what constitutes negative?
machine-learning
dna-sequence
blast
updated 5 months ago by
Ram
43k • written 7.6 years ago by
nafizh
• 0
4
votes
9
replies
580
views
variant calling
variant-calling
updated 25 days ago by
Ram
43k • written 26 days ago by
dalibenam64
• 0
0
votes
9
replies
1.1k
views
grep multiple lines form file
shell-script
grep
updated 10 months ago by
Ram
43k • written 4.0 years ago by
harry
▴ 30
2
votes
9
replies
1.1k
views
Read length for single -ended RNA seq data analysis
read-length
fastq
updated 9 months ago by
Ram
43k • written 9 months ago by
vinaya
• 0
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
dthorbur
★ 1.9k • written 3 months ago by
fish_enthusiast
• 0
1
vote
9
replies
1.2k
views
Trying to edit VCF file
VCF
R
bcftools
snpsaurus
updated 10 months ago by
Ram
43k • written 10 months ago by
peavy
• 0
0
votes
9
replies
596
views
99.9999% of Q30 bases is normal?
RNA-seq
fastp
updated 16 days ago by
LauferVA
4.2k • written 18 days ago by
Aki
▴ 20
1
vote
9
replies
1.5k
views
blast retrieves "N/A" for taxonomic data
blast
blastn
updated 7 weeks ago by
flavianegrete
• 0 • written 3.4 years ago by
langziv
▴ 50
1
vote
9
replies
531
views
miRNA alignment with Bowtie2
bowtie2
6 weeks ago by
Chironex
▴ 40
2
votes
9
replies
846
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 4 days ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
6
votes
9
replies
2.0k
views
Error when runing Bowtie2: (ERR): bowtie2-align exited with value 1
BAM
Bowtie
updated 11 months ago by
Ram
43k • written 15 months ago by
luzglongoria
▴ 50
0
votes
9
replies
1.2k
views
Normalization across different single cell RNAseq experimetns
global-scaling
single-cell
scRNA-seq
batch-effect
updated 11 days ago by
Ram
43k • written 3.9 years ago by
jmah
▴ 20
0
votes
9
replies
2.4k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome
nanopore
basecalling
fastq
updated 4 hours ago by
chujie
• 0 • written 8 months ago by
Gio
• 0
2
votes
9
replies
1.2k
views
Salmon (or other pseudo-mappers) for multi-species RNAseq read filtering
STAR
Salmon
mapper
aligner
RNAseq
5 months ago by
ian.will
▴ 30
0
votes
9
replies
541
views
Low number of both surviving reads after trimming
trimmomatic
trimming
4 weeks ago by
Jay
• 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
3.3k
views
build databses for genome using snpEff
annotation
SNP
snpEff
updated 8 months ago by
nehakhilwani18
• 0 • written 5.7 years ago by
StudentBio
• 0
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
ATpoint
82k • written 5.0 years ago by
Joel Wallenius
▴ 210
3
votes
9
replies
793
views
Understanding this analysis pipeline
reads
updated 10 months ago by
Ram
43k • written 10 months ago by
artemchuki
• 0
1
vote
9
replies
1.4k
views
Couldn't get a file descriptor referring to the console multiqc
multiqc
updated 11 months ago by
Ram
43k • written 22 months ago by
smithkthedale
▴ 10
4
votes
9
replies
1.2k
views
Snakemake issue with wrappers
Python
Snakemake
5 months ago by
Begonia_pavonina
▴ 150
7
votes
8
replies
9.0k
views
Determining read count
trimmomatic
rna-seq
trinity
updated 8 months ago by
Ram
43k • written 8.0 years ago by
nikelle.petrillo
▴ 110
0
votes
8
replies
563
views
STAR aligner options
STAR
4 weeks ago by
theophile
• 0
1
vote
8
replies
3.4k
views
Best way to address different batches of RNA-seq
sequence
RNA-Seq
RPKM
Fold-Change
batch-effect
updated 11 days ago by
Ram
43k • written 7.0 years ago by
tud55122
▴ 20
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
ido.idobar
▴ 10 • written 3 months ago by
Elizabeth
▴ 30
4
votes
8
replies
2.0k
views
How to extract promoter sequences from a plant draft genome?
promoter
genome
updated 11 months ago by
Ram
43k • written 4.6 years ago by
Kumar
▴ 120
0
votes
8
replies
1.5k
views
Cannot find Output files after applying Markduplicates with picard tools
picard-tools
MarkDuplicates
updated 6 weeks ago by
xiangbinruan
• 0 • written 19 months ago by
Phoebe Magdy
• 0
7
votes
8
replies
4.2k
views
DEseq2 design matrix with 3 factors
RNA-seq
deseq2
updated 10 months ago by
Ram
43k • written 3.9 years ago by
kand3e
▴ 60
1
vote
8
replies
1.1k
views
Shannon's Entropy by Sliding Window in R
Sequence
Window
R
Entropy
Sliding
updated 10 months ago by
rohitsatyam102
▴ 850 • written 17 months ago by
Alex
• 0
1
vote
8
replies
1.5k
views
counts of cite-seq-count vs. cellrenager varies tremendously
citeseq-count
cellranger
cite-seq
scRNA-seq
updated 4 months ago by
ATpoint
82k • written 9 months ago by
Assa Yeroslaviz
★ 1.8k
3
votes
8
replies
909
views
Can these RNAseq runs be combined?
transcriptomics
replicates
RNAseq
updated 10 months ago by
GenoMax
141k • written 10 months ago by
mdrnao
• 0
1
vote
8
replies
3.9k
views
No gene can be mapped
R
GSEA
updated 4 months ago by
jv
★ 1.8k • written 2.3 years ago by
yang.zhizhang
• 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
1
vote
8
replies
1.1k
views
How does one access TCGA controlled data in AWS S3?
tcga
aws
updated 6 months ago by
Zhenyu Zhang
★ 1.2k • written 6 months ago by
Cmouli
▴ 10
0
votes
8
replies
1.9k
views
Chromosome Location of Sequence in Fasta File using Biopython
biopython
python
updated 10 months ago by
Ram
43k • written 4.4 years ago by
muhammad.khizerkiet
• 0
5
votes
8
replies
3.7k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression
RNA-seq
gene-ontology
updated 19 days ago by
Ram
43k • written 6.5 years ago by
firestar
★ 1.6k
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
Ram
43k • written 7.1 years ago by
AJTrunkskun94
• 0
3
votes
8
replies
985
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
Ram
43k • written 2.4 years ago by
Lucía
• 0
1
vote
8
replies
977
views
Reads in IGV are mostly in intron regions
Patchseq
RNA-seq
10 months ago by
Kai_Qi
▴ 130
5
votes
8
replies
1.9k
views
looking for tools to detect RNA contamination in DNA
RNA-Seq
DNA-Seq
contamination
QC
updated 6 months ago by
Jingjingzhang
• 0 • written 3.7 years ago by
from the mountains
▴ 230
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
1,000 results • Page
3 of 20
Recent Votes
Comment: NGS forensics: how to know if data is fabricated
A: Hard time trying to calculate Allele Frequency and DP from Platypus
Answer: 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
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: 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
▴ 530
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?
Answer: What does it mean single base resolution in sequencing?
by
LauferVA
4.2k
Hi @fe3e6f65 , In a single sentence, the answer to your question can be summarized as, "*the resolution of a genomic technology refers to …
Comment: PCA plot
by
LauferVA
4.2k
Without more context, we cannot interpret this PCA plot. There are many possibilities. In addition, this question is basic enough that it w…
Comment: NGS forensics: how to know if data is fabricated
by
Jeremy Leipzig
22k
i have the name ready: out**liar**
Comment: What does it mean single base resolution in sequencing?
by
GenoMax
141k
Sequencing by hybridization (https://en.wikipedia.org/wiki/Sequencing_by_hybridization ) is likely not giving you single base resolution. B…
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