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36 results • Page
1 of 1
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0
votes
0
replies
1
view
Finding common pattern among heterogenous group of cancer
rnaseq
sequencing
just now by
Hyper_Odin
▴ 240
0
votes
0
replies
13
views
How to compare two sequence logo?
bioinformatics
31 minutes ago by
Andrew Liu
▴ 10
0
votes
2
replies
61
views
Clustered, annotated dotplot to scRNA-Seq data
scRNA-Seq
dotplot
visualization
updated 30 minutes ago by
Friederike
8.4k • written 4 hours ago by
tomer9w
• 0
0
votes
0
replies
6
views
Snakemake cluster execution error
cluster
snakemake
conda
50 minutes ago by
blackadder
• 0
0
votes
1
reply
14
views
doubts about SNAP, bioinformatic tools for gene prediction
gene
prediction
updated 31 minutes ago by
lieven.sterck
14k • written 54 minutes ago by
JUAN LUIS
• 0
0
votes
1
reply
89
views
Computationally generated transcriptional regulation network
GRN
updated 1 hour ago by
Matthias Zepper
▴ 910 • written 12 hours ago by
nicoyanovsky
• 0
2
votes
5
replies
46
views
Forum:
Getting the best of RNA-Seq
RNA-Seq
isoform
gene
expression
updated just now by
GenoMax
117k • written 1 hour ago by
Antonio R. Franco
★ 4.8k
0
votes
0
replies
11
views
News:
online training - Data Visualization with Python
Visualization
Python
Data
1 hour ago by
carlopecoraro2
★ 2.1k
0
votes
1
reply
139
views
How to count the number of multimapped reads from a bam file?
rnaseq
mapping
bowtie2
featurecounts
updated 1 hour ago by
Shred
▴ 640 • written 2 days ago by
O.rka
▴ 600
0
votes
2
replies
45
views
How to find average read length and number of reads in a bam file using samtools in linux?
bam
sequencing
read
samtools
46 minutes ago by
MobiusT
• 0
1
vote
2
replies
49
views
Tool similar to CollectGcBiasMetrics
metrics
picards
bioinformatics
gcbias
tool
1 hour ago by
tea.vuki
▴ 10
0
votes
3
replies
91
views
Align short sequence against ONT reads
reads
ONT
long
genome
alignment
updated 33 minutes ago by
Friederike
8.4k • written 6 hours ago by
kirillkirilenko.tomsk
• 0
0
votes
0
replies
40
views
Gene ontology enrichment vs. REACTOME pathway analysis
GO
REACTOME
4 hours ago by
Gene_MMP8
▴ 210
0
votes
0
replies
36
views
News:
Cellosaurus release 42 is available
line
cell
biocuration
knowledgebase
database
5 hours ago by
Amos Bairoch
▴ 110
0
votes
0
replies
34
views
mRNA contamination in miRNA prep
RIN
miRNA
5 hours ago by
Abhishek
• 0
0
votes
0
replies
32
views
extract rRNA/tRNA and other ncRNA ratio in a table from small RNA-seq
non-coding
small
RNA-seq
miRNA
analysis
RNA
clustering
5 hours ago by
Rey
• 0
0
votes
0
replies
36
views
TCGA CIMP status
Bioinformatics
TCGA
COAD
6 hours ago by
ilomilo
• 0
1
vote
1
reply
81
views
Question regarding normalization in Seurat
Seurat
scRNAseq
updated 3 hours ago by
ATpoint
62k • written 6 hours ago by
ylin575
▴ 10
0
votes
0
replies
67
views
PCA and logistic regression in GWAS
logistic
GWAS
PCA
regression
13 hours ago by
gosssheen
• 0
0
votes
2
replies
94
views
PCA plot for miRNA
miRNA
PCA
3 hours ago by
struggler
• 0
0
votes
6
replies
162
views
Ribosomal Depletion
rRNA
STAR
sequencing
contamination
RNA
updated 13 hours ago by
andres.firrincieli
★ 2.5k • written 16 hours ago by
kcarery
• 0
0
votes
1
reply
112
views
Error with TCGA package - TCGAbiolinks
TCGA
r
cancer
updated 11 hours ago by
Kevin Blighe
81k • written 20 hours ago by
JACKY
▴ 10
0
votes
0
replies
58
views
Question about rMATS output files
rMATS
novel
20 hours ago by
Lillian
• 0
1
vote
6
replies
298
views
ESTIMATE tumor purity
purity
r
cancer
20 hours ago by
JACKY
▴ 10
1
vote
6
replies
210
views
Exctract unmapped reads from BLAST
blatella
unmapped
germanica
annotation
blast
trinotate
16 hours ago by
Pilar
• 0
4
votes
3
replies
4.5k
views
Resfams Database usage
Resfams
updated 22 hours ago by
Neel
▴ 10 • written 6.1 years ago by
ginna
▴ 10
0
votes
1
reply
82
views
Searching for RNA-seq melanoma samples in TCGA or cBioPortal
TCGA
r
cBioPortal
cancer
updated 30 minutes ago by
Friederike
8.4k • written 1 day ago by
JACKY
▴ 10
0
votes
1
reply
150
views
SRA obtained metagenomic reads appears to corrupt - cannot work on SingleM
SingleM
SRAtoolkit
updated 21 hours ago by
GenoMax
117k • written 1 day ago by
rfour92
• 0
1
vote
3
replies
209
views
Quick way to get a field such as QNAME from the last read in a bam file?
bam
samtools
updated 20 minutes ago by
Friederike
8.4k • written 2 days ago by
kalavattam
▴ 70
0
votes
4
replies
212
views
how to get a sequence from read fragments with ref sequence?
reads
fragments
reference
assembly
sequence
4 hours ago by
Aaron
• 0
2
votes
3
replies
404
views
Determine sex/ gender of a mouse cell line via sequencing data
sequencing
line
cell
updated 4 hours ago by
Amos Bairoch
▴ 110 • written 6 weeks ago by
cwwong13
▴ 10
0
votes
2
replies
210
views
fineSTRUCTURE Resources
fineSTRUCTURE
populationgenomics
STRUCTURE
SNP
updated 7 hours ago by
Juan MONROY-NIETO
• 0 • written 8 weeks ago by
loeba
• 0
0
votes
23
replies
1.3k
views
Computing allele frequencies per individual for a set of SNPs in PLINK
plink
frequencies
allele
11 minutes ago by
pifferdavide
▴ 100
2
votes
12
replies
1.7k
views
6 follow
PROVEAN not working
provean
updated 5 hours ago by
YuFeng
• 0 • written 2.0 years ago by
AnnaW
▴ 20
1
vote
3
replies
1.1k
views
Survival analysis based on a set of genes for TCGA data
tcga
r
RNA-Seq
survival
updated 1 minute ago by
yussufhajjaj93
• 0 • written 19 months ago by
fifty_fifty
▴ 30
26
votes
10
replies
23k
views
Sjdboverhang Option In Star
updated 7 hours ago by
Thind amarinder
▴ 260 • written 8.3 years ago by
Martombo
★ 2.9k
36 results • Page
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Recent Votes
Answer: bash script for merging R1 and R2 reads
Answer: Question regarding normalization in Seurat
Gzip output of fasterq-dump
DESeq2 converting numeric to factor for unknown reason - SOLVED
DESeq2 converting numeric to factor for unknown reason - SOLVED
Tool similar to CollectGcBiasMetrics
pathway mapping of annotated genes (of bacteria)
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Recent Replies
Comment: Getting the best of RNA-Seq
by
Antonio R. Franco
★ 4.8k
By rational means that after running a GO enrichment, you ended with a set of reasonable set of transcripts (not genes) that could related …
Comment: Getting the best of RNA-Seq
by
Antonio R. Franco
★ 4.8k
This is the actual problem. If you are using as reference for the mapping a fasta file containing isoforms, your analysis should be address…
Comment: Quick way to get a field such as QNAME from the last read in a bam file?
by
Friederike
8.4k
If these are unsorted files, why would you need the last read? Couldn't you pick a random read or the first one?
Comment: Getting the best of RNA-Seq
by
Friederike
8.4k
>To mention, I started to use Kallisto and DESeq2 to see that after importing the data with the tximport package using the txOut = FALSE or…
Comment: Searching for RNA-seq melanoma samples in TCGA or cBioPortal
by
Friederike
8.4k
Can you specify a bit more what the end goal is? I.e. what type of data (processed, raw, ...) would you like to download and what would you…
Comment: Align short sequence against ONT reads
by
Friederike
8.4k
Are the long reads very different from each other (e.g. covering different regions of the genome) or do they all represent the same (more o…
Answer: Clustered, annotated dotplot to scRNA-Seq data
by
Friederike
8.4k
The [`dittoSeq`](https://github.com/dtm2451/DittoSeq) package also offers a [`dotPlot` function](http://bioconductor.org/packages/release/b…
Comment: doubts about SNAP, bioinformatic tools for gene prediction
by
lieven.sterck
14k
Hello https://www.biostars.org/u/110969/, Welcome to the forum! Please use the formatting bar (especially the `code` option) to present y…
Comment: How to find average read length and number of reads in a bam file using samtools
by
MobiusT
• 0
The size is 24661059 and I waited aroun 10 mins
Comment: Getting the best of RNA-Seq
by
ATpoint
62k
It is unclear to me what the question is. Do you want gene-level or transcript-level analysis? From what I know gene level analysis does no…
Answer: Computationally generated transcriptional regulation network
by
Matthias Zepper
▴ 910
Unfortunately, I have no experience whatsoever with yeast or GRN, but I recall [this article by de Boer et al.][1] that might be helpful. I…
Comment: Tool similar to CollectGcBiasMetrics
by
tea.vuki
▴ 10
it runs for a very long time, i wanted to know whether there's some shorter-running alternative
Comment: Tool similar to CollectGcBiasMetrics
by
Pierre Lindenbaum
146k
what's wrong with this tool ?
Comment: How to find average read length and number of reads in a bam file using samtools
by
Pierre Lindenbaum
146k
duplicate of your previous question : https://www.biostars.org/p/9528211/ > I used first samtools stats file.bam | grep "average length" b…
Answer: How to count the number of multimapped reads from a bam file?
by
Shred
▴ 640
Your question title doesn't fit properly the question body: please fix it. You're not counting multimapping reads based on your command s…
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