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
1.3k
views
How can I count aminoacid residues from a HUGE compressed fasta file?
sequence
3.4 years ago by
schlogl
▴ 150
8
votes
20
replies
1.8k
views
Converting runpsipred Script to Work on Windows OS
psipred
windows
updated 12 months ago by
Ram
39k • written 4.8 years ago by
Bara'a
▴ 270
8
votes
20
replies
1.8k
views
Getting read depth for normal and tumour
R
WGS
vcf
4.2 years ago by
fi1d18
★ 4.2k
5
votes
20
replies
3.3k
views
DiscoSnp Segmentation fault
snp
discosnp
updated 8 months ago by
Ram
39k • written 7.8 years ago by
Hans
▴ 130
6
votes
20
replies
5.6k
views
filling of missing genotype information in merged variant call vcf file
SNP
5.0 years ago by
princy149
▴ 80
9
votes
20
replies
3.4k
views
Solve SAM issues flagged by Picard's ValidateSamFile
Picard
SAM
updated 9 weeks ago by
Ram
39k • written 4.8 years ago by
marongiu.luigi
▴ 680
8
votes
20
replies
2.3k
views
Why does cufflinks split this transcript?
RNA-Seq
cufflinks
assembly
5.4 years ago by
corend
▴ 70
5
votes
20
replies
7.4k
views
How to plot ChIP-seq Density vs Distance from TSS using Homer annoted files
ChIP-Seq
homer
6.8 years ago by
varsha619
▴ 90
6
votes
19
replies
2.2k
views
Clustering for Single-cell RNA-seq Data
clustering
R
single-cell
3.8 years ago by
aloke205
▴ 40
0
votes
19
replies
1.1k
views
map fasts files
RNA-Seq
FASTQ
R
5.3 years ago by
Learner
▴ 260
5
votes
19
replies
1.3k
views
how I can come up with a permanent error
R
software error
6.1 years ago by
fi1d18
★ 4.2k
7
votes
19
replies
2.4k
views
mapping script process sleeping on server.
alignment
updated 12 months ago by
Ram
39k • written 8.2 years ago by
lvogel
▴ 30
9
votes
19
replies
1.7k
views
There are any way to use a script for feed emboss with fasta sequence?
sequence
3.4 years ago by
schlogl
▴ 150
0
votes
19
replies
1.1k
views
best blast strategy: read vs cluster?
alignment
blast
search
strategy
3.5 years ago by
marongiu.luigi
▴ 680
7
votes
19
replies
6.4k
views
[R] Microarray analysis interpreting logFC after makeContrasts
microarray
R
updated 16 months ago by
Ram
39k • written 8.6 years ago by
mheiser1
▴ 10
10
votes
19
replies
2.6k
views
What is a difference between uniprot and 'nr. Non-redundant GenBank...'?
Genebank
blast
UniProt
updated 2.0 years ago by
GenoMax
129k • written 2.0 years ago by
matt
▴ 20
17
votes
19
replies
2.2k
views
Sorting sequences according header
software error
sequence
Assembly
next-gen
6.8 years ago by
Gian77
▴ 60
0
votes
19
replies
2.1k
views
error related to vcfstats
numpy
snp
vcf
vcfstats
22 months ago by
rheab1230
▴ 140
0
votes
19
replies
8.3k
views
Skip orientation as there are not enough pairs by bwa mem
whole genome
bwa
paired end sequencing
4.0 years ago by
seta
★ 1.8k
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
4
votes
19
replies
2.5k
views
Use machine learning as classifier
R
rRNA
16S
18S
ITS
updated 5.7 years ago by
Biostar
20 • written 5.9 years ago by
cool.abbecker
▴ 30
22
votes
19
replies
2.5k
views
targets of a list of miRNAs
miRNAs
RNA-Seq
DEanalysis
target-prediction
6.6 years ago by
fi1d18
★ 4.2k
6
votes
19
replies
1.3k
views
Fastq header modification
sequence
next-gen
updated 5.2 years ago by
Ram
39k • written 5.2 years ago by
Guillaume
• 0
0
votes
19
replies
3.3k
views
Difficulty installing GATKtoolkit
GATK
Variant calling
SNPs
Indels
5.4 years ago by
jaqx008
▴ 110
3
votes
19
replies
4.9k
views
gatk-launch file missing
next-gen
sequencing
software error
updated 4.1 years ago by
finswimmer
16k • written 4.1 years ago by
sruthi
▴ 40
0
votes
19
replies
1.2k
views
scatterplot in R
microarray
expression
gene
updated 7 months ago by
Ram
39k • written 8 months ago by
bioinformatics
▴ 10
1
vote
19
replies
5.8k
views
Conda install package - different internals
R
software error
updated 3.8 years ago by
Biostar
20 • written 3.8 years ago by
lihe.liu
▴ 30
1
vote
19
replies
1.6k
views
High no feature counts in ht-seq counts
RNA-Seq
sequencing
4.5 years ago by
eozcan
▴ 10
15
votes
19
replies
1.4k
views
trimmomaric command for a fasta file?
trimmomatic
updated 5.1 years ago by
Ram
39k • written 5.1 years ago by
Nadin.asal
• 0
13
votes
19
replies
4.5k
views
bbmerge not joining paired-end reads
bbmerge
alignment
5.5 years ago by
bioplanet
▴ 60
2
votes
18
replies
5.3k
views
No differentially expressed genes using DESeq2
RNA-Seq
deseq2
6.5 years ago by
Sumit Paliwal
▴ 40
2
votes
18
replies
1.8k
views
I need help in this
gene
weblems
alignment
updated 10 months ago by
Ram
39k • written 7.4 years ago by
efosa15
• 0
16
votes
18
replies
4.1k
views
8 follow
Python Program to read .fasta file to .txt file
Python
updated 3.8 years ago by
Mensur Dlakic
★ 23k • written 3.8 years ago by
tikshyadav19
• 0
3
votes
18
replies
2.1k
views
Help creating Deseq2 count matrix from separate files
or
Sample
matrix
updated 22 months ago by
Ram
39k • written 23 months ago by
Nai
▴ 50
4
votes
18
replies
3.4k
views
Significance of reads mapping to Viruses - FusionCatcher
RNA-Seq
virus
reads
fusion
updated 9 months ago by
Ram
39k • written 7.5 years ago by
Joel TM
▴ 60
7
votes
18
replies
4.0k
views
Bowtie indexing of a fasta file that consists of a large amount of sequences
bowtie
alignment
genome
6.6 years ago by
valerie
▴ 100
7
votes
18
replies
7.7k
views
9 follow
Cuffmerge running error
RNA-Seq
updated 15 months ago by
Ram
39k • written 8.5 years ago by
hana
▴ 190
14
votes
18
replies
4.2k
views
GATK Haplotype Caller
next-gen
GATK
haplotype
caller
contigs
updated 6.4 years ago by
Biostar
20 • written 6.6 years ago by
plink_9857
▴ 50
4
votes
18
replies
12k
views
Alignment with BWA and SAMtools
BWA
SAM-file
SAMtools
updated 2.6 years ago by
Biostar
20 • written 4.8 years ago by
Shelle
▴ 30
0
votes
18
replies
1.0k
views
No gene name after annovar vcf file processing
vcf
annovar
3.6 years ago by
valerie
▴ 100
4
votes
18
replies
2.6k
views
Inline barcodes in the reverse reads
barcodes
6.6 years ago by
Picasa
▴ 640
5
votes
18
replies
5.3k
views
EnhancedVolcano plot error: Log2foldchange is not numeric!
R
EnhancedVolcano
3.5 years ago by
michelle.piquet
▴ 60
1
vote
18
replies
2.2k
views
Why big gaps when I use Entrez Eutils to download protein coding sequences.
entrez
eutils
6.8 years ago by
Tom
▴ 40
7
votes
18
replies
4.0k
views
Fold change UP and Down in dplyr calculation
R
5.8 years ago by
1769mkc
★ 1.1k
1
vote
18
replies
1.2k
views
Find tissues that are functionally related
tissue
functionally-related
gene-expression
updated 3.7 years ago by
Biostar
20 • written 3.8 years ago by
Natasha
▴ 40
3
votes
18
replies
1.1k
views
6 follow
What sequencing/alignment artifact is this?
variants
mutect
sequencing
alignment
mitochondria
7 months ago by
lacb
▴ 120
2
votes
18
replies
1.9k
views
Bwa on multiple processor
np
mpirun
bwa
alignment
16 months ago by
shivangi.agarwal800
▴ 120
0
votes
18
replies
1.3k
views
freebayes error variant calling
snp
2.8 years ago by
evelyn
▴ 220
20
votes
17
replies
5.1k
views
HiSeq 4000 PhiX screening and removal using bbduk
spikein
filtering
bbmap
bbduk
phix
5.8 years ago by
Anand Rao
▴ 560
0
votes
17
replies
1.1k
views
Transcripts with no read support
RNA-Seq
alignment
assembly
salmon
2.7 years ago by
Dunois
★ 2.3k
1,000 results • Page
2 of 20
Recent Votes
Comment: Regular Expression for conversion
Answer: RNAseq Data and Pipeline
Comment: Salmon Index
Comment: Salmon Index
Resequencing data of pangenome
A: PolyPhen Humdiv vs HumVar discrepancies
A: How To Get Annotation For Bed File From Another Bed File
Recent Locations •
All
Republic of Ireland,
1 minute ago
United Kingdom,
1 minute ago
United States,
1 minute ago
United States,
6 minutes ago
United States,
6 minutes ago
United States,
7 minutes ago
Germany,
7 minutes ago
Recent Awards •
All
Popular Question
to
tarek.mohamed
▴ 350
Popular Question
to
carlopecoraro2
★ 2.3k
Popular Question
to
kamanovae
▴ 80
Popular Question
to
Lila M
★ 1.2k
Popular Question
to
oakhamwolf
▴ 20
Commentator
to
Istvan Albert
98k
Voter
to
Martin
▴ 20
Recent Replies
Comment: Unusual FASTQ file
by
Ram
39k
People from the middle east/indian subcontinent often associate the term "post title" with their job title, because a) post translates more…
Comment: How to make a dotplot for bulk RNA average expression ?
by
bhumm
▴ 40
I am not entirely clear on what you are trying to accomplish, but based on @Trivas answer, I would first transform the data relative to ave…
Answer: What is the best way to clean bulk RNA-seq data?
by
swbarnes2
13k
There really is no "best". Just find something reasonable, and document what you chose.
Comment: How to deal with duplicated gene IDs in TCGA RNA expression data?
by
Vincent Laufer
★ 2.8k
ok interesting. Do all, most, some, or a few of the genes have repeated lines. Is there a handy link to the exact file you are looking at?
Answer: Make a BedGraph file
by
bhumm
▴ 40
Bedtools window piped into genomecov? https://bedtools.readthedocs.io/en/latest/content/tools/window.html https://bedtools.readthedocs.io…
Answer: RNAseq Data and Pipeline
by
ATpoint
72k
STAR counts are the raw counts, that is appropriate for DESeq2.
Comment: RNAseq Data and Pipeline
by
swbarnes2
13k
STAR has a GeneCounts output that looks as you describe; three columns, depending on whether one thinks the prep is unstranded, or stranded…
Comment: RNAseq Data and Pipeline
by
Ram
39k
There is at least one more step that you haven't shared, isn't there? This line alone does not get you the data. You don't need to give us …
Comment: RNAseq Data and Pipeline
by
turcoa1
• 0
my entire code is not done. All I am trying to understand is if the STAR - counts downloaded from this query have raw reads. There are head…
Comment: RNAseq Data and Pipeline
by
Ram
39k
Please provide your entire code so those of us wishing to do a quick test can download and check for ourselves. Also, please use the format…
Comment: RNAseq Data and Pipeline
by
turcoa1
• 0
```r query <- GDCquery( project = "TCGA-THCA", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantificatio…
Comment: NCBI Common Taxonomy Tree
by
GenoMax
129k
It may be best to email NCBI help desk with these questions. Post their response here once you hear back from them.
Comment: RNAseq Data and Pipeline
by
Ram
39k
What data are you downloading? Can you show us your GDCquery commands please?
Comment: Salmon Index
by
ashleymb1116
• 0
I am working on cow, Bos Taurus. The Arabidopsis code was an example code that was on Salmon's github and an example for indexing they gave…
Comment: Salmon Index
by
GenoMax
129k
> I am using the Bos Taurus files Which organism are you actually working on? You have mentioned three so far, arabidopsis, human and now …
Traffic: 2591 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