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1,000 results • Page
4 of 20
Sort: replies
Rank
Views
Votes
Replies
12
votes
22
replies
2.5k
views
Help with error in GATK variant calling
GATK
updated 11 months ago by
Ram
43k • written 11 months ago by
Chris
▴ 260
57
votes
22
replies
28k
views
7 follow
Batch correction in DESeq2
Combat
DESeq2
Batch-Effect
updated 19 days ago by
Ram
43k • written 4.5 years ago by
Arindam Ghosh
▴ 510
27
votes
22
replies
5.7k
views
8 follow
Forum:
Recommendations of Linux distros for beginners in bioinformatics
training
linux
updated 11 months ago by
Ram
43k • written 6.4 years ago by
ropolocan
▴ 810
138
votes
22
replies
65k
views
15 follow
How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental Biologist/non-bioinformatician
gene
LIMMA
edgeR
updated 10 months ago by
Kevin Blighe
87k • written 6.4 years ago by
Mike
★ 1.9k
9
votes
22
replies
9.7k
views
Tool:
BioLabDonkey - new Mac program for molecular biologists
software
biolabdonkey
9 months ago by
vytarasov
▴ 180
38
votes
21
replies
19k
views
8 follow
Tool:
pybam - 100% python BAM reader
python
htspython
bam
pysam
updated 10 months ago by
Ram
43k • written 8.0 years ago by
John
13k
39
votes
21
replies
13k
views
10 follow
Forum:
Orientation of PE reads a review of --fr --ff and --rf meanings
RNA-Seq
updated 11 months ago by
Ram
43k • written 5.5 years ago by
Juke34
8.5k
27
votes
21
replies
38k
views
12 follow
Converting a VCF with SNPs and indels to BED format
next-gen
updated 6 months ago by
Axzd
▴ 70 • written 9.8 years ago by
onter
▴ 170
18
votes
21
replies
4.4k
views
Tool:
uQ - small binary FASTQ
Compression
FASTQ
updated 10 months ago by
Ram
43k • written 7.1 years ago by
John
13k
80
votes
21
replies
36k
views
17 follow
How to know that your RNA-seq is stranded or not?
RNA-Seq
updated 5 months ago by
kathryn.jacksonjones
• 0 • written 10.0 years ago by
M K
▴ 660
4
votes
21
replies
2.3k
views
6 follow
how to automate this process
python
plantCARE
updated 10 months ago by
Ram
43k • written 7.2 years ago by
ashish
▴ 680
16
votes
21
replies
9.9k
views
7 follow
How to extract bigWig signal for a given bed file?
bigWig
updated 8 months ago by
Ram
43k • written 7.5 years ago by
Bioradical
▴ 60
10
votes
21
replies
3.2k
views
How to interpret heatmap using plotheatmap from deeptools?
ATAC-seq
deeptools
8 months ago by
Chris
▴ 260
24
votes
21
replies
7.5k
views
9 follow
News:
Misunderstood parameter of NCBI BLAST
blast
alignment
updated 11 months ago by
Ram
43k • written 5.6 years ago by
Farbod
★ 3.4k
4
votes
21
replies
2.7k
views
Limma returned only positive logFC values
edgeR
differential-expression
deg
limma
10 months ago by
melissachua90
▴ 60
48
votes
21
replies
5.1k
views
9 follow
What Online Gene-Centric Resources Do You Use?
gene
database
updated 5 months ago by
Ram
43k • written 14.0 years ago by
Andrew Su
4.9k
43
votes
21
replies
5.4k
views
9 follow
Helping Biostar Grow
biostars
updated 5 months ago by
Ram
43k • written 14.0 years ago by
Eric Normandeau
11k
12
votes
21
replies
6.6k
views
7 follow
Illumina HumanHT-12 V4.0 expression beadchip
R
lumi
LIMMA
updated 5 months ago by
Gordon Smyth
★ 7.0k • written 4.1 years ago by
zelda
▴ 50
14
votes
21
replies
10k
views
7 follow
HOMER annotatePeaks.pl problem
RNA-Seq
ChIP-Seq
HOMER
updated 10 months ago by
Ram
43k • written 6.6 years ago by
Seq225
▴ 110
13
votes
21
replies
3.0k
views
6 follow
Aberrant splicing in bulk RNAseq
aberrant-splicing
transcript
isoform
exon
updated 11 months ago by
sbt_gvs
• 0 • written 14 months ago by
txema.heredia
▴ 110
15
votes
21
replies
5.5k
views
7 follow
alphafold online availability and use case
alphafold
structure
prediction
written 2.7 years ago by
gnmcsbnfrmtcsclb
▴ 70
60
votes
21
replies
3.8k
views
14 follow
Reproduce the article "The complete sequence of a human genome."
genome
assembly
updated 7 months ago by
Michael
54k • written 7 months ago by
sqshigg
▴ 60
22
votes
21
replies
4.8k
views
7 follow
Quick Programming Challenge: Calculate Common And Unique Regions From A List Of Chromosome Segments
programming
updated 5 months ago by
Ram
43k • written 14.0 years ago by
Khader Shameer
18k
5
votes
21
replies
2.9k
views
How to get my tool on Homebrew ?
homebrew
pipeline
updated 10 months ago by
Ram
43k • written 4.8 years ago by
Elephantdumbo
▴ 20
0
votes
21
replies
1.1k
views
Expression analysis of LncRNA from RNA-seq data
expression
lncrna
10 weeks ago by
analyst
▴ 30
52
votes
21
replies
49k
views
11 follow
Fastq Splitter For Paired End Reads
rna
updated 10 months ago by
Ram
43k • written 12.1 years ago by
Geparada
★ 1.5k
23
votes
21
replies
8.8k
views
9 follow
fastest UMAP method
UMAP
R
updated 5 months ago by
Mensur Dlakic
★ 27k • written 4.5 years ago by
grey
▴ 30
81
votes
21
replies
42k
views
15 follow
How To Get Bed File Containing Exons Of Canonical Transcripts And Their Corresponding Gene Symbols
bed
transcript
ucsc
biomart
updated 7 months ago by
Joel Wallenius
▴ 210 • written 10.2 years ago by
pristanna
▴ 750
13
votes
21
replies
1.8k
views
Practical Haplotype Graph Paths
practical-haplotype-graph
PHG
updated 11 weeks ago by
pjb39
▴ 200 • written 5 months ago by
micah_k
▴ 10
21
votes
20
replies
9.2k
views
11 follow
Laptops for bioinformatics
hardware
Laptops
updated 10 months ago by
LauferVA
4.2k • written 17 months ago by
tsomakiank
▴ 40
16
votes
20
replies
14k
views
7 follow
Extracting allele, Genotype from VCF file
vcf
updated 10 months ago by
Ram
43k • written 6.0 years ago by
sukhjindermultani85
▴ 20
7
votes
20
replies
6.4k
views
7 follow
Repeat masked gtf files from ensembl
ensembl
RNA-Seq
genome
updated 13 days ago by
e.r.zakiev
▴ 200 • written 4.3 years ago by
kevin.stachelek
▴ 80
22
votes
20
replies
4.8k
views
Tool:
elPrep 4.0.0, a high-performance drop-in replacement tool for GATK4/Picard/SAMtools for processing SAM/BAM files
sam
bam
bqsr
updated 10 months ago by
Ram
43k • written 5.5 years ago by
Charlotte.Herzeel
▴ 150
83
votes
20
replies
19k
views
17 follow
How Do Pathway Databases Compare?
pathway
database
subjective
updated 9 months ago by
Peter Karp
▴ 30 • written 13.5 years ago by
Shigeta
▴ 470
7
votes
20
replies
2.1k
views
Forum:
NGS RNA-Seq Analysis Pipeline Tophat vs STAR
STAR
RNA-Seq
TopHat
updated 11 months ago by
Ram
43k • written 3.3 years ago by
mikefeixu
▴ 10
29
votes
20
replies
3.7k
views
Tool:
FastQt : a clone of FastQC in C++/Qt
fastqc
Cpp
fastq
Qt
updated 10 months ago by
Ram
43k • written 7.4 years ago by
sacha
★ 2.4k
14
votes
20
replies
6.7k
views
7 follow
Tool Recommendations For Human Genome Assembly
assembly
human-genome
updated 10 months ago by
Ram
43k • written 11.2 years ago by
Chris Cole
▴ 800
28
votes
20
replies
21k
views
7 follow
how do I run repeat masker
repeatmasker
updated 3 months ago by
Andrzej Zielezinski
11k • written 8.4 years ago by
ksi216
▴ 80
0
votes
20
replies
1.6k
views
Rockhoppper - Suspiciously low percentage of perfectly aligned reads
Rockhopper
RNA-seq
6 months ago by
langziv
▴ 50
18
votes
20
replies
4.1k
views
9 follow
Is There Any Useful Information To Be Gathered Analyzing The Genomes Of Different Populations Of Cicadas?
project
education
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Scott
▴ 70
18
votes
20
replies
4.4k
views
6 follow
How to identify significant differentially expressed genes and gene regulatory networks from microarray data.
microarray
differential-gene-expression
updated 15 days ago by
Ram
43k • written 7.5 years ago by
morteza.mahmoudisaber
▴ 80
17
votes
20
replies
1.4k
views
What is the best way to compute genetic distances between FASTQ files?
genetic-distance
fastq
updated 5 months ago by
GenoMax
141k • written 6 months ago by
mikazon
▴ 10
12
votes
20
replies
2.4k
views
SEACR and MACS2
MACS2
SEACR
updated 9 months ago by
rfran010
▴ 900 • written 10 months ago by
qudrat.nii
▴ 10
15
votes
20
replies
1.7k
views
Bbtools callvariant multisample mode, + base recalibration
Bbtools
5 months ago by
Axzd
▴ 70
0
votes
20
replies
1.6k
views
How can I obtain the DNA sequences of each CDS for several genbank files?
genbank
DNA
sequence
4 months ago by
Raphaëlle
• 0
5
votes
20
replies
4.2k
views
Differential gene expression from RNAseq data. Before or after annotation?
differential-gene-expression
RNA-seq
updated 15 days ago by
Ram
43k • written 6.2 years ago by
pablo61991
▴ 90
2
votes
20
replies
2.3k
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
7 months ago by
Maxine
▴ 40
12
votes
20
replies
1.2k
views
Help with gatk BaseRecalibrator
GATK
variant-calling
updated 4 months ago by
Ram
43k • written 4 months ago by
Chris
▴ 260
1
vote
20
replies
1.6k
views
randomreads.sh only produces reads for chr1 to chr7
randomreads.sh
bbmap
updated 9 months ago by
GenoMax
141k • written 10 months ago by
berndmann
▴ 10
37
votes
20
replies
7.2k
views
14 follow
Online Bioinformatics Resources
online-resources
updated 5 months ago by
Ram
43k • written 14.0 years ago by
Eric Normandeau
11k
1,000 results • Page
4 of 20
Recent Votes
Comment: clustalo - align milions of short seq, memory issue
Comment: downloading genomes in fasta format from accession ids
Comment: PCA plot (Suggestions Needed)
Answer: PCA plot (Suggestions Needed)
PCA plot (Suggestions Needed)
Comment: To get p-values for the TPM
A: Where To Download Pam50 Gene Set?
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Recent Replies
Answer: clustalo - align milions of short seq, memory issue
by
emmanouil.a
▴ 120
Hi GenoMax and Mensur Dlakic, thank you for your feedback. I'm changing approach in the way to work with a smaller number of seq.
Comment: Annovar using R package
by
Pierre Lindenbaum
161k
duplicate of your previous question: https://www.biostars.org/p/9592646/ why using R when there are shell-based tools like VEP ? slivar , …
Comment: Trouble with Pilon installation
by
Lissa Cruz Saavedra
• 0
Hi I am trying to install the software but I didn't find the way to clone from github. Could you help me with the pipeline of instruction…
Comment: Adding CB tag to bam file
by
swbarnes2
14k
I think both these programs are just adding the same tag to every line. I don't think either cares whether it's called RG or CB
Comment: PCA plot (Suggestions Needed)
by
swbarnes2
14k
Even if this was real data, the tiny numbers for the PC1 and PC2 indicate that the differences between the samples are all absolutely tiny.…
Comment: Creating Synthetic Sequences for a ML Model
by
biochugs
• 0
Thanks for the input. I'll continue to think of more ideas that may be achievable.
Comment: PCA plot (Suggestions Needed)
by
Jeremy
▴ 890
You could also try kernel PCA, which is a non-linear form of PCA, although this will be more time-consuming.
Comment: Troubleshooting RNA-seq data with DNA contamination
by
DKA
▴ 40
I have unstranded RNA-seq data. Please share the tool with me, if you do not mind.
Comment: PCA plot (Suggestions Needed)
by
Mensur Dlakic
★ 27k
Everything that @f1f58aed said, plus that there may be no data manipulation that will give you the clusters you expected. Sometimes there a…
Answer: Creating Synthetic Sequences for a ML Model
by
Mensur Dlakic
★ 27k
It is a good idea, though I don't see how it would work in practice. I think you will encounter at least one additional problem on top of …
Answer: PCA plot (Suggestions Needed)
by
Jeremy
▴ 890
Right now, the WT samples are clustering together, but you have one mutant sample off by itself, which could be an outlier. How did you sc…
Comment: Adding CB tag to bam file
by
GenoMax
141k
@yokofakun had written this: https://www.biostars.org/p/336965/ https://github.com/ruqianl/appendCB may also be useful.
Comment: Troubleshooting RNA-seq data with DNA contamination
by
GenoMax
141k
Please post information about your tool as a `tools` category post. Don't wait/ask other users to ask you.
Comment: Adding CB tag to bam file
by
Maria
• 0
Sorry for the delay in my answer, I got sidetracked. I am using ```samtools addreplacerg -r "@RG\tID:$cell" -o $cell.bam -h $LINE``` bu…
Answer: Troubleshooting RNA-seq data with DNA contamination
by
haibol2017
▴ 10
We just developed a R package to tackle this problem. Do you have stranded or unstranded RNA-seq data contaminated with gDNA? If you wou…
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