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1,000 results • Page
1 of 20
Sort: Votes
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Views
Votes
Replies
23
votes
22
replies
40k
views
6 follow
Converting VCF to PLINK .bed binary fileset to check for pedigree errors with KING: How do conversion tools make the PLINK .fam file, without asking …
plink
vcf
fam
gatk
vcftools
updated 6 months ago by
Nicole
• 0 • written 5.1 years ago by
gaelgarcia
▴ 250
22
votes
20
replies
2.1k
views
what is the prefered strategy to treat with blast-less transcriptomes from RNA-seq
blast
RNA-Seq
genome
gene
updated 7 weeks ago by
Ram
39k • written 6.9 years ago by
Farbod
★ 3.4k
20
votes
15
replies
26k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink
SNP
updated 10 months ago by
Ram
39k • written 7.4 years ago by
dam4l
▴ 190
18
votes
4
replies
8.2k
views
How To Find Rna-Seq Data Of Published Papers?
geo
next-gen
RNA-seq
updated 3 months ago by
Ram
39k • written 9.8 years ago by
user
▴ 930
18
votes
19
replies
1.7k
views
6 follow
Extremely important marker gene has many reads based on IGV viewer but no quantified reads
rna-seq
sequencing
igv
alignment
next-gen
updated 6 months ago by
Ram
39k • written 4.4 years ago by
rbkh09
• 0
18
votes
7
replies
901
views
How to calculate if statistically a variable of a bulk RNA-seq affects the comparison of interest?
DESeq2
Variable
RNA-seq
8 months ago by
Rafael Soler
★ 1.2k
16
votes
8
replies
1.7k
views
8 follow
What are the most important unresolved problems in Bioinformatics?
bioinformatics
updated 7 weeks ago by
Ram
39k • written 6.7 years ago by
chen
★ 2.4k
14
votes
5
replies
2.8k
views
bioinformatics basic training
genome
updated 11 weeks ago by
Ram
39k • written 8.5 years ago by
f.muoghalu
• 0
12
votes
8
replies
699
views
Align 16S sequence to a reference
16S
sequence
alignment
updated 8 months ago by
Matthias Zepper
3.7k • written 8 months ago by
A_heath
▴ 140
12
votes
4
replies
493
views
Annotating TSS: By Transcript or by Gene? Code Validation Help Needed!
genome
bed
transcript
TSS
17 days ago by
Rafael Soler
★ 1.2k
12
votes
13
replies
2.2k
views
Gene Expression and Systems Biology (homework)
gene
homework
updated 5 months ago by
Ram
39k • written 7.9 years ago by
sarathkurichiyil
• 0
11
votes
9
replies
2.1k
views
samtools piping with awk/ bash commands -> Wonky things happen!!!
bash
samtools
awk
updated 5 months ago by
Ram
39k • written 8.0 years ago by
QVINTVS_FABIVS_MAXIMVS
★ 2.5k
10
votes
5
replies
6.5k
views
how to remove asterisk characters from a translated sequences (fasta format)?
sequencing
Assembly
alignment
updated 9 months ago by
Ram
39k • written 7.8 years ago by
seta
★ 1.8k
10
votes
11
replies
8.3k
views
How to adjust my manhattan plot to look better?
qqman
manhattan
R
updated 12 months ago by
Ram
39k • written 8.2 years ago by
SheelS
▴ 40
10
votes
15
replies
5.3k
views
convert fasta/gb to vcf
fasta
vcf
genbank
gff
updated 10 weeks ago by
Ram
39k • written 4.7 years ago by
marongiu.luigi
▴ 680
10
votes
8
replies
1.9k
views
Blast scores...two annotations for the same piece of sequence
alignment
updated 11 months ago by
Ram
39k • written 8.2 years ago by
friasoler
▴ 30
10
votes
6
replies
2.6k
views
which language to use for such a bioinformatics web services infrastructure?
web-services
java
updated 10 weeks ago by
Ram
39k • written 8.0 years ago by
lait
▴ 170
10
votes
1
reply
3.2k
views
RNA-SeQC, EVER-seq, RSeQC and CollectRnaSeqMetrics, which to use and *why*?
RNA-Seq
qc
updated 9 months ago by
Ram
39k • written 8.0 years ago by
Niek De Klein
★ 2.6k
9
votes
4
replies
1.9k
views
[Code] Converte fasta/fa files to fastq
perl
fastq
sed
fasta
updated 9 months ago by
Ram
39k • written 7.5 years ago by
Shicheng Guo
★ 9.3k
9
votes
2
replies
395
views
Answer needed urgently
Deep
updated 8 months ago by
Mensur Dlakic
★ 23k • written 8 months ago by
Deepak
• 0
9
votes
4
replies
5.3k
views
How to analyse normalized read count?
RNA-Seq
R
updated 4 months ago by
Ram
39k • written 8.0 years ago by
pbio
▴ 150
9
votes
1
reply
5.6k
views
Why does MACS2 report multiple records for the same peak region?
ChIP-Seq
macs
macs2
updated 9 months ago by
Ram
39k • written 7.6 years ago by
James Ashmore
★ 3.4k
9
votes
7
replies
853
views
Reference genome location
reference
positions
FASTA
alignment
genome
updated 4 months ago by
barslmn
★ 1.5k • written 5 months ago by
Batel
• 0
9
votes
4
replies
466
views
RNA seq, secreted protein
protein
gene
secreted
updated 5 months ago by
Joe
21k • written 5 months ago by
Rob
▴ 160
9
votes
9
replies
1.7k
views
Which hg38 file?
reference
hg38
NCBI
updated 9 months ago by
appropiate
▴ 80 • written 10 months ago by
amy__
▴ 50
9
votes
20
replies
3.4k
views
Solve SAM issues flagged by Picard's ValidateSamFile
Picard
SAM
updated 10 weeks ago by
Ram
39k • written 4.8 years ago by
marongiu.luigi
▴ 680
9
votes
16
replies
3.0k
views
6 follow
covert SAM to full length fasta
fasta
SAM
updated 10 weeks ago by
Ram
39k • written 4.8 years ago by
marongiu.luigi
▴ 680
9
votes
4
replies
1.5k
views
On which branch in bioinformatics should a cancer researcher focus on ?
cancer
updated 7 weeks ago by
Ram
39k • written 6.8 years ago by
Bilal
▴ 60
8
votes
13
replies
891
views
Mapped reads not mapping to a real sequence?
bam
sam
samtools
kallisto
3 months ago by
txema.heredia
▴ 70
8
votes
9
replies
2.6k
views
error in rstudio
csv
matrix
rstudio
updated 8 months ago by
Ram
39k • written 7.8 years ago by
fi1d18
★ 4.2k
8
votes
4
replies
1.7k
views
using different tools to identify differential exprssed genes
rna-seq
RNA-Seq
R
updated 8 months ago by
Ram
39k • written 7.8 years ago by
Anushka
▴ 20
8
votes
9
replies
2.2k
views
6 follow
Big difference in estimated duplicate reads between forward and reverse of paired-end RNA-seq
RNA-Seq
duplication
fastqc
updated 11 months ago by
rohitsatyam102
▴ 690 • written 3.6 years ago by
Eric Lim
★ 2.1k
8
votes
12
replies
2.7k
views
Use BLAST Command Line Applications to run a folder of many sequences against a database
BLAST
updated 10 weeks ago by
Ram
39k • written 21 months ago by
daver.v
▴ 30
8
votes
6
replies
833
views
How to apply bioinformatic in vaccine design?
Vaccine
updated 6 months ago by
Dunois
★ 2.3k • written 6 months ago by
Jean
▴ 50
8
votes
5
replies
11k
views
samtools tview symbols
samtools
updated 6 months ago by
Ram
39k • written 7.9 years ago by
biolab
★ 1.4k
8
votes
5
replies
3.2k
views
Is it possible to guess sequencing platform used based on a FASTQ/BAM file?
BAM
FASTQ
updated 5 months ago by
Ram
39k • written 7.9 years ago by
Andrew
▴ 60
8
votes
25
replies
2.1k
views
construction of a database
sql
noSQL
neo4j
database
updated 10 weeks ago by
Ram
39k • written 2.0 years ago by
Debut
▴ 20
8
votes
11
replies
1.3k
views
using STAR instead of HISAT2
STAR
updated 10 months ago by
Ram
39k • written 10 months ago by
Chris
▴ 100
8
votes
2
replies
6.1k
views
Differential gene expression analysis in Python
python
R
updated 3 months ago by
Ram
39k • written 19 months ago by
Leendert
▴ 30
8
votes
3
replies
618
views
Package installation error using Bioconda
antismash
Bioconda
5 months ago by
A_heath
▴ 140
8
votes
3
replies
5.0k
views
Bioinformatics project for a beginner
projects
updated 10 months ago by
Ram
39k • written 7.5 years ago by
dharshank.1096
▴ 30
7
votes
7
replies
4.4k
views
RNA-Seq time series analysis using a DESeq2 spline approach yields far too many significant genes
splines
DESeq2
time-series
RNA-Seq
updated 2 days ago by
Ram
39k • written 4.4 years ago by
stu111538
▴ 80
7
votes
4
replies
1.3k
views
So many Zeros (read counting)_NGS sequence analysis with R / Bioconductor: RNA-Seq workflow
alignment
RNA-Seq
R
updated 11 weeks ago by
Ram
39k • written 4.9 years ago by
healing80
• 0
7
votes
2
replies
3.1k
views
Counting reads for gene transcripts with overlapping loci
RNA-Seq
gene
R
updated 4 months ago by
Ram
39k • written 8.0 years ago by
Ruet
▴ 70
7
votes
16
replies
2.1k
views
Insert size selection for RNASeq data: does it make sense?
RNA-Seq
sequencing
updated 9 weeks ago by
Ram
39k • written 5.6 years ago by
Matteo Schiavinato
★ 3.6k
7
votes
3
replies
748
views
Using a Docker image with ensembl-vep
Linux
ensembl-vep
Docker
updated 5 months ago by
barslmn
★ 1.5k • written 5 months ago by
langziv
▴ 30
7
votes
10
replies
1.3k
views
Ubuntu 20.04 Crash
Ubuntu
updated 3 months ago by
Ram
39k • written 16 months ago by
bala
• 0
7
votes
8
replies
3.4k
views
remove duplicated entries from BLAST result file
blast
alignment
updated 5 months ago by
Ram
39k • written 8.0 years ago by
Kumar
▴ 160
7
votes
8
replies
2.4k
views
Discrepency between number of reads tophat
RNA-Seq
tophat
software-error
updated 8 months ago by
Ram
39k • written 7.8 years ago by
mbio.kyle
▴ 380
7
votes
8
replies
1.7k
views
How can we time a recent gene duplication event using (neutral?) DNA mutations as molecular clock?
molecular-clock
gene-duplication
phylogeny
updated 3 months ago by
Ram
39k • written 8.1 years ago by
xiaofeng.dong12
▴ 20
1,000 results • Page
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Recent Votes
Comment: including samples for which group is unknown to help adjust for another variable
Answer: ggsave() bug in ggplot2?
Comment: ggsave() bug in ggplot2?
Comment: ggsave() bug in ggplot2?
A: What is a suitable LD threshold for LD pruning of snp data?
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Answer: how to sort a fasta file
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Recent Replies
Comment: including samples for which group is unknown to help adjust for another variable
by
Vincent Laufer
★ 2.9k
Actually, I just remembered the perfect paper to illustrate that idea. Look at this: https://pubmed.ncbi.nlm.nih.gov/35976223/. In this man…
Comment: including samples for which group is unknown to help adjust for another variable
by
Vincent Laufer
★ 2.9k
yep! updated my answer to respond to this. i think they ARE biological variables. it is understanding the nature of those variables that is…
Answer: ggsave() bug in ggplot2?
by
Medeea
• 0
I think the issue is solved with saving the file as .png There must be a problem with the .jpg format then. Thanks everyone for the va…
Comment: ggsave() bug in ggplot2?
by
Ram
39k
Try PDF. You won't need dpi for that. Also, do things work well if you use the lower level `png(); ggplot(); dev.off();` sequence instead o…
Comment: How to calculate kinship matrix table from vcf file
by
chrchang523
10k
The last vcftools release was in 2018. It has been superseded by bcftools for most purposes, and by plink 1.9/2.0 for most analytical func…
Comment: NarrowPeak format -Peak field
by
ATpoint
72k
I do not follow, can you please add a chr-start-end example.
Comment: BioPython: convert fasta to fastq without quality score input file
by
capemaster
• 0
The command with `gawk` is: awk 'BEGIN {RS = ">" ; FS = "\n"} NR > 1 {print $1"\n"$2"\n+\n"gensub(/./, "I", "g", $2)}'
Comment: The inchworm process failed. Trinity running error.
by
GenoMax
129k
So with 600M reads you will need a minimum of 600GB of RAM per trinity recommendations. If you are not able to get more memory consider no…
Comment: How GATK pipeline called a homozygeous alternate allele (1/1) although one copy
by
Ram
39k
I don't understand what you're saying. Your allele is different from the ref allele so it needs the sample to support that? Why? Give me t…
Comment: How GATK pipeline called a homozygeous alternate allele (1/1) although one copy
by
mohsamir2016
▴ 30
Sure, but n my case 1/1 the allel is different from the reference allele and it called it as T, for instance. So it needs reads in the samp…
Comment: The inchworm process failed. Trinity running error.
by
andres.firrincieli
3.3k
can you run the same command with just one sample with the flag `--verbose` so we can actually see the error?
Comment: ggsave() bug in ggplot2?
by
Medeea
• 0
Thank you very much for your suggestion, I have tried with units = "cm" and still it is not saved at desired dpi. I also ran your example …
Comment: How GATK pipeline called a homozygeous alternate allele (1/1) although one copy
by
Ram
39k
I've removed irrelevant tags from your post.
Answer: How GATK pipeline called a homozygeous alternate allele (1/1) although one copy
by
Ram
39k
Ref alleles are from the reference genome. GATK doesn't need a read supporting the ref genome on a sample to know what the ref base is at a…
Comment: Single Cell Rna Seq Using BD Rhapsody
by
Ram
39k
What does this have to do with Rhapsody scRNA? Also, why are you recommending DESeq2 for scRNA DE analysis?
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