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
7
votes
21
replies
2.7k
views
Merged.gtf vs. Rnor_6.0.gtf for Raw Counts
RNA-Seq
cuffmerge
raw counts
7.1 years ago by
jmsyl.hong
• 0
22
votes
20
replies
2.3k
views
what is the prefered strategy to treat with blast-less transcriptomes from RNA-seq
blast
RNA-Seq
genome
gene
updated 7 months ago by
Ram
41k • written 7.4 years ago by
Farbod
★ 3.4k
8
votes
20
replies
2.4k
views
Getting read depth for normal and tumour
R
WGS
vcf
4.7 years ago by
fi1d18
★ 4.2k
0
votes
20
replies
1.3k
views
Rockhoppper - Suspiciously low percentage of perfectly aligned reads
Rockhopper
RNA-seq
6 weeks ago by
langziv
▴ 50
5
votes
20
replies
3.8k
views
DiscoSnp Segmentation fault
snp
discosnp
updated 14 months ago by
Ram
41k • written 8.3 years ago by
Hans
▴ 140
6
votes
20
replies
6.1k
views
filling of missing genotype information in merged variant call vcf file
SNP
5.5 years ago by
princy149
▴ 80
9
votes
20
replies
3.8k
views
Solve SAM issues flagged by Picard's ValidateSamFile
Picard
SAM
updated 8 months ago by
Ram
41k • written 5.3 years ago by
marongiu.luigi
▴ 690
5
votes
20
replies
8.0k
views
How to plot ChIP-seq Density vs Distance from TSS using Homer annoted files
ChIP-Seq
homer
7.3 years ago by
varsha619
▴ 90
4
votes
20
replies
1.6k
views
How can I count aminoacid residues from a HUGE compressed fasta file?
sequence
3.9 years ago by
schlogl
▴ 160
8
votes
20
replies
2.7k
views
Why does cufflinks split this transcript?
RNA-Seq
cufflinks
assembly
5.9 years ago by
corend
▴ 70
2
votes
20
replies
1.8k
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
12 weeks ago by
Maxine
▴ 40
8
votes
20
replies
2.2k
views
Converting runpsipred Script to Work on Windows OS
psipred
windows
updated 18 months ago by
Ram
41k • written 5.3 years ago by
Bara'a
▴ 270
6
votes
19
replies
2.6k
views
Clustering for Single-cell RNA-seq Data
clustering
R
single-cell
4.3 years ago by
aloke205
▴ 40
3
votes
19
replies
1.1k
views
Systematic errors at the end and beginning of reads in NGS panels
NGS
error
panels
sequencing
updated 5 months ago by
Asaf
10k • written 5 months ago by
captainlabman
▴ 10
1
vote
19
replies
6.5k
views
Conda install package - different internals
R
software error
updated 4.3 years ago by
Biostar
20 • written 4.3 years ago by
lihe.liu
▴ 30
4
votes
19
replies
2.9k
views
Use machine learning as classifier
R
rRNA
16S
18S
ITS
updated 6.2 years ago by
Biostar
20 • written 6.4 years ago by
cool.abbecker
▴ 30
7
votes
19
replies
6.7k
views
[R] Microarray analysis interpreting logFC after makeContrasts
microarray
R
updated 22 months ago by
Ram
41k • written 9.1 years ago by
mheiser1
▴ 10
15
votes
19
replies
1.7k
views
trimmomaric command for a fasta file?
trimmomatic
updated 5.6 years ago by
Ram
41k • written 5.6 years ago by
Nadin.asal
• 0
0
votes
19
replies
1.2k
views
map fasts files
RNA-Seq
FASTQ
R
5.8 years ago by
Learner
▴ 270
0
votes
19
replies
1.3k
views
best blast strategy: read vs cluster?
alignment
blast
search
strategy
4.0 years ago by
marongiu.luigi
▴ 690
7
votes
19
replies
2.7k
views
mapping script process sleeping on server.
alignment
updated 18 months ago by
Ram
41k • written 8.7 years ago by
lvogel
▴ 30
10
votes
19
replies
3.0k
views
What is a difference between uniprot and 'nr. Non-redundant GenBank...'?
Genebank
blast
UniProt
updated 2.5 years ago by
GenoMax
136k • written 2.5 years ago by
matt
▴ 20
17
votes
19
replies
2.5k
views
Sorting sequences according header
software error
sequence
Assembly
next-gen
7.3 years ago by
Gian77
▴ 60
22
votes
19
replies
2.9k
views
targets of a list of miRNAs
miRNAs
RNA-Seq
DEanalysis
target-prediction
7.1 years ago by
fi1d18
★ 4.2k
13
votes
19
replies
5.0k
views
bbmerge not joining paired-end reads
bbmerge
alignment
6.0 years ago by
bioplanet
▴ 60
0
votes
19
replies
9.1k
views
Skip orientation as there are not enough pairs by bwa mem
whole genome
bwa
paired end sequencing
4.5 years ago by
seta
★ 1.8k
6
votes
19
replies
1.5k
views
Fastq header modification
sequence
next-gen
updated 5.7 years ago by
Ram
41k • written 5.7 years ago by
Guillaume
• 0
3
votes
19
replies
5.6k
views
gatk-launch file missing
next-gen
sequencing
software error
updated 4.6 years ago by
finswimmer
16k • written 4.6 years ago by
sruthi
▴ 40
1
vote
19
replies
1.8k
views
High no feature counts in ht-seq counts
RNA-Seq
sequencing
5.0 years ago by
eozcan
▴ 10
5
votes
19
replies
1.6k
views
how I can come up with a permanent error
R
software error
6.6 years ago by
fi1d18
★ 4.2k
18
votes
19
replies
2.0k
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 12 months ago by
Ram
41k • written 4.9 years ago by
rbkh09
• 0
0
votes
19
replies
2.5k
views
error related to vcfstats
numpy
snp
vcf
vcfstats
2.3 years ago by
rheab1230
▴ 140
0
votes
19
replies
1.7k
views
scatterplot in R
microarray
expression
gene
updated 14 months ago by
Ram
41k • written 14 months ago by
bioinformatics
▴ 20
9
votes
19
replies
2.0k
views
There are any way to use a script for feed emboss with fasta sequence?
sequence
3.9 years ago by
schlogl
▴ 160
0
votes
19
replies
3.6k
views
Difficulty installing GATKtoolkit
GATK
Variant calling
SNPs
Indels
5.9 years ago by
jaqx008
▴ 110
2
votes
18
replies
5.8k
views
No differentially expressed genes using DESeq2
RNA-Seq
deseq2
7.0 years ago by
Sumit Paliwal
▴ 40
3
votes
18
replies
2.7k
views
Help creating Deseq2 count matrix from separate files
or
Sample
matrix
updated 2.4 years ago by
Ram
41k • written 2.4 years ago by
Nai
▴ 50
14
votes
18
replies
4.6k
views
GATK Haplotype Caller
next-gen
GATK
haplotype
caller
contigs
updated 6.9 years ago by
Biostar
20 • written 7.1 years ago by
plink_9857
▴ 50
0
votes
18
replies
1.6k
views
freebayes error variant calling
snp
3.3 years ago by
evelyn
▴ 220
5
votes
18
replies
6.1k
views
EnhancedVolcano plot error: Log2foldchange is not numeric!
R
EnhancedVolcano
4.0 years ago by
michelle.piquet
▴ 60
3
votes
18
replies
1.5k
views
6 follow
What sequencing/alignment artifact is this?
variants
mutect
sequencing
alignment
mitochondria
13 months ago by
lacb
▴ 120
2
votes
18
replies
2.3k
views
Bwa on multiple processor
np
mpirun
bwa
alignment
23 months ago by
shivangi.agarwal800
▴ 120
0
votes
18
replies
1.3k
views
bcl2fastq conversion with specifying exact match of indices
genome
RNA-Seq
sequencing
updated 3 months ago by
GenoMax
136k • written 3 months ago by
Apex92
▴ 280
0
votes
18
replies
1.3k
views
No gene name after annovar vcf file processing
vcf
annovar
4.1 years ago by
valerie
▴ 100
1
vote
18
replies
2.4k
views
Why big gaps when I use Entrez Eutils to download protein coding sequences.
entrez
eutils
7.3 years ago by
Tom
▴ 40
4
votes
18
replies
15k
views
Alignment with BWA and SAMtools
BWA
SAM-file
SAMtools
updated 3.1 years ago by
Biostar
20 • written 5.3 years ago by
Shelle
▴ 30
1
vote
18
replies
1.5k
views
Find tissues that are functionally related
tissue
functionally-related
gene-expression
updated 4.2 years ago by
Biostar
20 • written 4.3 years ago by
Natasha
▴ 40
4
votes
18
replies
3.8k
views
Significance of reads mapping to Viruses - FusionCatcher
RNA-Seq
virus
reads
fusion
updated 15 months ago by
Ram
41k • written 8.0 years ago by
Joel TM
▴ 60
4
votes
18
replies
2.8k
views
Inline barcodes in the reverse reads
barcodes
7.1 years ago by
Picasa
▴ 640
16
votes
18
replies
5.0k
views
8 follow
Python Program to read .fasta file to .txt file
Python
updated 4.3 years ago by
Mensur Dlakic
★ 25k • written 4.3 years ago by
tikshyadav19
• 0
1,000 results • Page
2 of 20
Recent Votes
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp
Seurat integration of two datasets - GSE126783
about batch correction in scRNA-seq
How to compare two Seurat object (sample) in order to find top markers?
How do I resolve an integration error in Seurat?
The difference between merge and integration with Seurat objects
Analyzing single cell RNA seq with multiple samples and conditions
Recent Locations •
All
Germany,
just now
Mexico,
1 minute ago
Spain,
3 minutes ago
Perth, Australia,
4 minutes ago
San Francisco,
6 minutes ago
Australia,
8 minutes ago
India,
9 minutes ago
Recent Awards •
All
Popular Question
to
mohammedtoufiq91
▴ 230
Popular Question
to
Mariah.Hoffman
▴ 20
Commentator
to
AK
★ 2.2k
Popular Question
to
wiscoyogi
▴ 40
Popular Question
to
Shicheng Guo
★ 9.3k
Popular Question
to
prasundutta87
▴ 660
Popular Question
to
massa.kassa.sc3na
▴ 590
Recent Replies
Comment: How can I map coordinates between two strains of yeast?
by
Jimmy
▴ 10
Yes (S. cerevisiae)
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp
by
GenoMax
136k
> less than 100 for some samples Hmm. That is surprising but then in light of that fact ~20% recovery of cells does not sound bad.
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp
by
newbee
▴ 40
Thanks for raising these valid points. I do not have the answer right now. Lately, I heard from the PI that they started with a small numbe…
Comment: How to get multiple protein domain database domain name from id's
by
GenoMax
136k
A list of InterPro domains is available: https://ftp.ebi.ac.uk/pub/databases/interpro/current_release/entry.list
Answer: DIAMOND tutorial
by
GenoMax
136k
`DIAMOND` has a wiki page: https://github.com/bbuchfink/diamond/wiki Links for DIAMOND papers are here: https://github.com/bbuchfink/diamo…
Comment: How to do simple pathway analysis?
by
AK
★ 2.2k
Hi [he1k](https://www.biostars.org/u/139817/), Please use the following script which downloads and parses the keg data on the fly: [keg_hi…
Comment: Is there a need to batch correct FPKM or TPM values for within sample comparison
by
CTLong
▴ 20
That's what I would assume, because we are not taking into account cross sample differences here. Thanks
Comment: Is there a need to batch correct FPKM or TPM values for within sample comparison
by
CTLong
▴ 20
That's a good point. So its probably safest to not batch correct for within sample comparisons I guess?
Answer: Generating count matrix from Chromium Fixed RNA Profiling (FRP) data outside Cel
by
MohammadAlkadi
▴ 70
What is the purpose of doing so? I tried to do that by using the bam file generated by CellRanger. One **important detail** if you are work…
Comment: Guidance on Crucial Parameters for Bioinformatic Analysis of Metabolomic Data
by
Kevin Blighe
86k
Thank you - appreciate the translation.
Answer: Guidance on Crucial Parameters for Bioinformatic Analysis of Metabolomic Data
by
Kevin Blighe
86k
Em geral, uma taxa de descoberta falsa de 5% (p ajustado<0,05 ) deve ser usada para qualquer teste estatístico em que múltiplas hipóteses i…
Answer: WGCNA tutorial docs needed: Horvath Lab site down
by
ATpoint
78k
See link here from the developer: https://bioinformatics.stackexchange.com/a/21886/16676
Comment: WGCNA tutorial docs needed: Horvath Lab site down
by
Katie
• 0
I would also appreciate the PDFs if anyone has them please
Answer: Loftee no splice site annotations
by
AMARU
• 0
Hey, did you solve it? I am having a very similar issue. Thanks
Answer: Bulk and Single Cell RNA-seq online course
by
swbarnes2
13k
I'd start by getting tutorials for R libraries like DESeq, EdgeR, Seurat, etc, and learn by doing.
Traffic: 1726 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