Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : all time
all time
today
this week
this month
this year
1,000 results • Page
2 of 20
Sort: replies
Rank
Views
Votes
Replies
4
votes
20
replies
1.5k
views
How can I count aminoacid residues from a HUGE compressed fasta file?
sequence
3.7 years ago by
schlogl
▴ 150
5
votes
20
replies
7.8k
views
How to plot ChIP-seq Density vs Distance from TSS using Homer annoted files
ChIP-Seq
homer
7.1 years ago by
varsha619
▴ 90
8
votes
20
replies
2.5k
views
Why does cufflinks split this transcript?
RNA-Seq
cufflinks
assembly
5.7 years ago by
corend
▴ 70
6
votes
20
replies
5.9k
views
filling of missing genotype information in merged variant call vcf file
SNP
5.3 years ago by
princy149
▴ 80
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 5 months ago by
Ram
40k • written 7.2 years ago by
Farbod
★ 3.4k
5
votes
20
replies
3.6k
views
DiscoSnp Segmentation fault
snp
discosnp
updated 11 months ago by
Ram
40k • written 8.1 years ago by
Hans
▴ 140
8
votes
20
replies
2.0k
views
Converting runpsipred Script to Work on Windows OS
psipred
windows
updated 16 months ago by
Ram
40k • written 5.2 years ago by
Bara'a
▴ 270
2
votes
20
replies
1.5k
views
The number of SVs called by `vg call` is much smaller than the number of SVs in the VCF used to construct the graph
vg
14 days ago by
Maxine
▴ 30
9
votes
20
replies
3.6k
views
Solve SAM issues flagged by Picard's ValidateSamFile
Picard
SAM
updated 6 months ago by
Ram
40k • written 5.1 years ago by
marongiu.luigi
▴ 690
8
votes
20
replies
2.2k
views
Getting read depth for normal and tumour
R
WGS
vcf
4.5 years ago by
fi1d18
★ 4.2k
6
votes
19
replies
2.4k
views
Clustering for Single-cell RNA-seq Data
clustering
R
single-cell
4.2 years ago by
aloke205
▴ 40
0
votes
19
replies
1.4k
views
scatterplot in R
microarray
expression
gene
updated 11 months ago by
Ram
40k • written 11 months ago by
bioinformatics
▴ 20
18
votes
19
replies
1.9k
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 9 months ago by
Ram
40k • written 4.7 years ago by
rbkh09
• 0
0
votes
19
replies
8.9k
views
Skip orientation as there are not enough pairs by bwa mem
whole genome
bwa
paired end sequencing
4.3 years ago by
seta
★ 1.8k
9
votes
19
replies
1.9k
views
There are any way to use a script for feed emboss with fasta sequence?
sequence
3.7 years ago by
schlogl
▴ 150
15
votes
19
replies
1.6k
views
trimmomaric command for a fasta file?
trimmomatic
updated 5.4 years ago by
Ram
40k • written 5.4 years ago by
Nadin.asal
• 0
1
vote
19
replies
1.7k
views
High no feature counts in ht-seq counts
RNA-Seq
sequencing
4.8 years ago by
eozcan
▴ 10
0
votes
19
replies
1.2k
views
map fasts files
RNA-Seq
FASTQ
R
5.6 years ago by
Learner
▴ 270
5
votes
19
replies
1.4k
views
how I can come up with a permanent error
R
software error
6.4 years ago by
fi1d18
★ 4.2k
6
votes
19
replies
1.4k
views
Fastq header modification
sequence
next-gen
updated 5.5 years ago by
Ram
40k • written 5.5 years ago by
Guillaume
• 0
0
votes
19
replies
3.5k
views
Difficulty installing GATKtoolkit
GATK
Variant calling
SNPs
Indels
5.7 years ago by
jaqx008
▴ 110
0
votes
19
replies
2.4k
views
error related to vcfstats
numpy
snp
vcf
vcfstats
2.1 years ago by
rheab1230
▴ 140
3
votes
19
replies
5.3k
views
gatk-launch file missing
next-gen
sequencing
software error
updated 4.4 years ago by
finswimmer
16k • written 4.4 years ago by
sruthi
▴ 40
4
votes
19
replies
2.7k
views
Use machine learning as classifier
R
rRNA
16S
18S
ITS
updated 6.1 years ago by
Biostar
20 • written 6.2 years ago by
cool.abbecker
▴ 30
3
votes
19
replies
830
views
Systematic errors at the end and beginning of reads in NGS panels
NGS
error
panels
sequencing
updated 11 weeks ago by
Asaf
10k • written 11 weeks ago by
captainlabman
• 0
7
votes
19
replies
6.6k
views
[R] Microarray analysis interpreting logFC after makeContrasts
microarray
R
updated 20 months ago by
Ram
40k • written 8.9 years ago by
mheiser1
▴ 10
13
votes
19
replies
4.8k
views
bbmerge not joining paired-end reads
bbmerge
alignment
5.8 years ago by
bioplanet
▴ 60
1
vote
19
replies
6.3k
views
Conda install package - different internals
R
software error
updated 4.1 years ago by
Biostar
20 • written 4.1 years ago by
lihe.liu
▴ 30
0
votes
19
replies
1.2k
views
best blast strategy: read vs cluster?
alignment
blast
search
strategy
3.8 years ago by
marongiu.luigi
▴ 690
22
votes
19
replies
2.7k
views
targets of a list of miRNAs
miRNAs
RNA-Seq
DEanalysis
target-prediction
7.0 years ago by
fi1d18
★ 4.2k
17
votes
19
replies
2.4k
views
Sorting sequences according header
software error
sequence
Assembly
next-gen
7.1 years ago by
Gian77
▴ 60
10
votes
19
replies
2.8k
views
What is a difference between uniprot and 'nr. Non-redundant GenBank...'?
Genebank
blast
UniProt
updated 2.3 years ago by
GenoMax
134k • written 2.4 years ago by
matt
▴ 20
7
votes
19
replies
2.6k
views
mapping script process sleeping on server.
alignment
updated 16 months ago by
Ram
40k • written 8.5 years ago by
lvogel
▴ 30
2
votes
18
replies
5.6k
views
No differentially expressed genes using DESeq2
RNA-Seq
deseq2
6.8 years ago by
Sumit Paliwal
▴ 40
7
votes
18
replies
4.4k
views
Fold change UP and Down in dplyr calculation
R
6.1 years ago by
1769mkc
★ 1.1k
0
votes
18
replies
1.2k
views
No gene name after annovar vcf file processing
vcf
annovar
3.9 years ago by
valerie
▴ 100
16
votes
18
replies
4.7k
views
8 follow
Python Program to read .fasta file to .txt file
Python
updated 4.1 years ago by
Mensur Dlakic
★ 24k • written 4.1 years ago by
tikshyadav19
• 0
2
votes
18
replies
2.0k
views
I need help in this
gene
weblems
alignment
updated 13 months ago by
Ram
40k • written 7.7 years ago by
efosa15
• 0
14
votes
18
replies
4.4k
views
GATK Haplotype Caller
next-gen
GATK
haplotype
caller
contigs
updated 6.7 years ago by
Biostar
20 • written 6.9 years ago by
plink_9857
▴ 50
4
votes
18
replies
3.6k
views
Significance of reads mapping to Viruses - FusionCatcher
RNA-Seq
virus
reads
fusion
updated 13 months ago by
Ram
40k • written 7.8 years ago by
Joel TM
▴ 60
4
votes
18
replies
2.7k
views
Inline barcodes in the reverse reads
barcodes
6.9 years ago by
Picasa
▴ 640
7
votes
18
replies
7.9k
views
9 follow
Cuffmerge running error
RNA-Seq
updated 19 months ago by
Ram
40k • written 8.9 years ago by
hana
▴ 190
3
votes
18
replies
2.5k
views
Help creating Deseq2 count matrix from separate files
or
Sample
matrix
updated 2.2 years ago by
Ram
40k • written 2.2 years ago by
Nai
▴ 50
3
votes
18
replies
1.4k
views
6 follow
What sequencing/alignment artifact is this?
variants
mutect
sequencing
alignment
mitochondria
11 months ago by
lacb
▴ 120
1
vote
18
replies
2.3k
views
Why big gaps when I use Entrez Eutils to download protein coding sequences.
entrez
eutils
7.1 years ago by
Tom
▴ 40
5
votes
18
replies
5.8k
views
EnhancedVolcano plot error: Log2foldchange is not numeric!
R
EnhancedVolcano
3.8 years ago by
michelle.piquet
▴ 60
7
votes
18
replies
4.2k
views
Bowtie indexing of a fasta file that consists of a large amount of sequences
bowtie
alignment
genome
6.9 years ago by
valerie
▴ 100
4
votes
18
replies
14k
views
Alignment with BWA and SAMtools
BWA
SAM-file
SAMtools
updated 2.9 years ago by
Biostar
20 • written 5.1 years ago by
Shelle
▴ 30
0
votes
18
replies
1.0k
views
bcl2fastq conversion with specifying exact match of indices
genome
RNA-Seq
sequencing
updated 28 days ago by
GenoMax
134k • written 29 days ago by
Apex92
▴ 270
0
votes
18
replies
1.5k
views
freebayes error variant calling
snp
3.1 years ago by
evelyn
▴ 220
1,000 results • Page
2 of 20
Recent Votes
Comment: Salmon index not progressing
Answer: Adding a control sample to bulk RNA-seq
Comment: Adding a control sample to bulk RNA-seq
Comment: kallisto normalized TPM values without bootstraps
Comment: Identify Alternative Splicing Event using exon and junction count table
Comment: Identify Alternative Splicing Event using exon and junction count table
Comment: Salmon index not progressing
Recent Locations •
All
Taiwan,
just now
New Zealand,
1 minute ago
United States,
2 minutes ago
Japan,
3 minutes ago
San Francisco,
9 minutes ago
Australia,
10 minutes ago
South Korea,
10 minutes ago
Recent Awards •
All
Teacher
to
seidel
11k
Popular Question
to
jabaron.phd
• 0
Commentator
to
ATpoint
76k
Scholar
to
GenoMax
134k
Popular Question
to
Morgan S.
▴ 80
Popular Question
to
paria
▴ 70
Popular Question
to
marongiu.luigi
▴ 690
Recent Replies
Comment: Salmon index not progressing
by
camillab.
▴ 130
I opened tow terminals and one was the code to build a decoy-aware transcriptome and the other was building indexes (no decoy)
Comment: Adding a control sample to bulk RNA-seq
by
Chris
▴ 180
Thank you for the explanation! So just want to confirm one control with replicate is totally useless even can't use as a reference?
Answer: DESeq2 analysis using two featureCounts generated from different studies
by
swbarnes2
13k
Comparing samples between labs is a bad idea. Better to generate gene lists from one study from one lab, and gene lists from another study…
Comment: Adding a control sample to bulk RNA-seq
by
swbarnes2
13k
If a sample wasn't prepared along side your treated samples, it is a different batch. If you had treated and controls in each of two diffe…
Comment: kallisto normalized TPM values without bootstraps
by
ATpoint
76k
You don't need sleuth. Typically these deconvolutions, or most downstream analysis, is done on the gene- rather than the transcript-level w…
Comment: Salmon index not progressing
by
ATpoint
76k
If the top $CPU column shows some values in the hundreds then it is doing something (actually when it's > 0%). So based on the screenshot i…
Comment: Salmon index not progressing
by
camillab.
▴ 130
Thank you. Waiting it's not gonna hurt me, when should I stop hoping and give up is the question? do you know is there a way if I can see i…
Comment: Filtering VCF to divide with equal sizes
by
Ram
40k
A more efficient way would be to make a 2 column CSV file, one column with the count value and the other with the chr:start-end range, then…
Answer: Filtering VCF to divide with equal sizes
by
avelarbio46
▴ 30
I divided my contigs using R, but it was more complex than the program Pierre Lindenbaum made (https://jvarkit.readthedocs.io/en/latest/Vcf…
Comment: Salmon index not progressing
by
ATpoint
76k
Just wait until it is finished. It's seems to be running. I just checked my logs and on our HPC with four cores such as process for a decoy…
Comment: Salmon index not progressing
by
GenoMax
134k
> 2 hrs trying to generate decoy-aware transcriptome for human. is this time normal? It is probably normal considering resources you have…
Comment: Chromosome bias on RNA-Seq differential gene expression analysis
by
grant.hovhannisyan
★ 2.5k
you expect to have aneuploidy only in the knockout?
Comment: STAR index not working
by
camillab.
▴ 130
thank you! I am following GenoMax suggestion and I am trying with `salmon` but it is stuck as well. it's not making any progress.....
Comment: Scanning for ultra-hot topics in science via pubmed, or using other tools
by
LauferVA
3.7k
@genomax , thank you. this is a really great start. i will likely use a python based approach, but other than that, i think ill proceed e…
Comment: OMA in AWS cloud
by
Ram
40k
> if it is possible. Yes, most things are possible on AWS. > I didn't find anything in the web. I *highly* **highly** doubt that.
Traffic: 2031 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6