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175 results • Page
4 of 4
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1
vote
3
replies
375
views
PCA plot
DESeq2
PCAplot
updated 4 days ago by
LauferVA
4.2k • written 8 days ago by
Aaliya
▴ 10
4
votes
4
replies
444
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 5 days ago by
BioinfGuru
★ 1.7k • written 8 days ago by
Ming Tommy Tang
★ 3.9k
0
votes
5
replies
365
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 5 days ago by
Istvan Albert
100k • written 9 days ago by
sehriban.buyukkilic
▴ 10
1
vote
1
reply
163
views
Including plasmid in alignment
Bacteria
Transcriptomics
BOWTIE2
STAR
2 days ago by
heelpPlease
• 0
5
votes
4
replies
343
views
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
22 hours ago by
Estevão
• 0
8
votes
16
replies
939
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 6 days ago by
bk11
★ 2.4k • written 8 weeks ago by
Sofia
• 0
2
votes
4
replies
274
views
from row count to tpm
tpm
row-count
normalization
updated 2 days ago by
Ram
43k • written 10 days ago by
michelafrancesconi9
▴ 20
1
vote
8
replies
445
views
Downsampling fastq file
downsample
fastq
2 days ago by
marco.barr
▴ 90
2
votes
3
replies
350
views
How to establish haplotype-specific gene expression levels
RNA-seq
Haplotype
updated 6 days ago by
dsull
★ 5.9k • written 23 days ago by
javanokendo
▴ 60
0
votes
10
replies
491
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 3 days ago by
i.sudbery
19k • written 10 days ago by
Patadu94
• 0
2
votes
11
replies
896
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 4 days ago by
jkbonfield
★ 1.2k • written 15 days ago by
me
• 0
1
vote
4
replies
254
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
1 hour ago by
eebloom
▴ 80
1
vote
0
replies
184
views
News:
Landscape Genomics course in Switzerland
LFMM
Landscape-Genomics
Sambada
R
Local-Adaptation
1 day ago by
carlopecoraro2
★ 2.5k
1
vote
2
replies
254
views
read length in structural variant calling
nanopore
SV
QC
ONT
variant
1 hour ago by
eebloom
▴ 80
0
votes
3
replies
331
views
CWl and toil singularity image e.g busybox? Thank you
toil
singularity
updated 3 days ago by
Ram
43k • written 4 months ago by
Fadi
• 0
1
vote
4
replies
1.0k
views
Filtering qscore on dorado
dorado
filtering
QC
nanopore
Guppy
22 hours ago by
eebloom
▴ 80
29
votes
28
replies
34k
views
11 follow
Split Fastq Files Into Chunks Of 1M Reads
split
fastq
updated 19 hours ago by
thomas.heigl.ibk
• 0 • written 12.8 years ago by
Bioscientist
★ 1.7k
2
votes
4
replies
2.6k
views
When to use .vcf or .gvcf files from GATK HaplotypeCaller?
indel
gatk
calling
snp
variant
updated 3 days ago by
Medhat
9.7k • written 24 months ago by
Vitor1
▴ 120
2
votes
5
replies
929
views
Retrieval of Active site information programmatically
Catalytic
Python
Active
PDB
site
Site
updated 3 days ago by
Wayne
★ 2.0k • written 2.0 years ago by
arinjoy
• 0
0
votes
1
reply
535
views
HOMER on AWS
HOMER
updated 9 hours ago by
clairechung112
• 0 • written 2.2 years ago by
Bogdan
★ 1.4k
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference
38build
impute
imputation
3 days ago by
anna
▴ 20
16
votes
12
replies
7.3k
views
10 follow
how to split multi-fasta file into single fasta file named by header
genome
perl
python3
bash
python
updated 3 hours ago by
rsieber
▴ 10 • written 3.1 years ago by
Kumar
▴ 120
1
vote
14
replies
2.3k
views
Extract gRNA sequence using cutadapt
cutadapt
trimming
crispr
sequencing
updated 15 hours ago by
GenoMax
142k • written 4.5 years ago by
Swimming bird
▴ 20
1
vote
6
replies
2.8k
views
Segmentation fault using gemma
gemma
gwas
updated 4 days ago by
dimpleadiwal050896
• 0 • written 4.9 years ago by
ggman
▴ 90
40
votes
10
replies
42k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma
sva
Combat
batch-effect
updated 3 days ago by
cwwong13
▴ 40 • written 6.7 years ago by
lessismore
★ 1.3k
175 results • Page
4 of 4
Recent Votes
Convert vcf files with phased genotypes to standard haplotype format
Convert vcf files with phased genotypes to standard haplotype format
A: Convert vcf files with phased genotypes to standard haplotype format
How to extract haplotype data from phased bcf files
How to extract haplotype data from phased bcf files
Answer: RNA-seq data for deep learning classification
Answer: Analysis of intronic reads included scRNA-seq data
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dsull
★ 5.9k
Scholar
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eebloom
▴ 80
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▴ 80
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Recent Replies
Comment: Downloading older version of a tool
by
GenoMax
142k
Have you tried conda install <pkg>=<version> so conda install smalt=0.5.8 <!-- junk -->
Comment: Generating mpileup file using samtools
by
Joe
21k
Older versions of software are usually available via distribution tools or the websites. It may require a lot of digging, but its almost ce…
Comment: RNA-seq data for deep learning classification
by
Yuju
• 0
Thank you very much for sharing your advice. Yes, it definitely makes sense that with the use of deep learning, models would learn normalis…
Comment: Generating mpileup file using samtools
by
Ruqaiya
• 0
I didn't use the same tool as in the paper...
Comment: read length in structural variant calling
by
eebloom
▴ 80
Yes good idea. I guess the quality of the SV calls and as a proxy for quality the length and distribution of variants called might be infor…
Comment: Generating mpileup file using samtools
by
Ruqaiya
• 0
I just realised I didn't align my reads with the tools they used and used bowtie2 instead. I can't download the older version that is menti…
Comment: Downsampling long-read BAM files
by
eebloom
▴ 80
This is not what I needed for this particular use case, as capping the coverage would lose the information on regions of copy number amplif…
Comment: Do I need to go back and filter my long-reads?
by
eebloom
▴ 80
Apologies, I deleted the question as I wasn't sure it would be helpful to others and it didn't seem to have a clear answer, not to snub the…
Comment: Do I need to go back and filter my long-reads?
by
eebloom
▴ 80
Thanks, I think it would be a good idea to track the results downstream to look for batch effects. I think I will filter the reads ultimate…
Comment: Generating mpileup file using samtools
by
ATpoint
82k
Seconding this. Apply current best practices (which is bcftools mpileup followed by something I forgot, see bcftools manual for variant cal…
Answer: Analysis of intronic reads included scRNA-seq data
by
ATpoint
82k
By default in CellRanger (lets assume you have 10x data processed with it) intronic reads are included. What you get in your matrix.mtx fil…
Comment: How does gene length effect the number of reads mapped
by
i.sudbery
19k
The number of reads for a gene is almost exactly linearly proportional to the length of the gene. In paired-end sequencing, we generally co…
Comment: What analysis suitable to identify similarly expressed genes between two samples
by
ATpoint
82k
Can you post your setup, so how many groups and their replication number? I can tell you by experience that you need even more replication …
Answer: DSEQ2 analysis
by
ATpoint
82k
The tool is called D**E**Seq2. Anyway, if your factor is `factor(conditions, levels = c("control", "mutant"))` then the first level is the …
Comment: Odd alignment question/finding
by
barslmn
★ 2.1k
Maybe it is caused by fastp. https://github.com/OpenGene/fastp/issues/506
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