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1,000 results • Page
5 of 20
Sort: replies
Rank
Views
Votes
Replies
15
votes
20
replies
1.6k
views
Bbtools callvariant multisample mode, + base recalibration
Bbtools
4 months ago by
Axzd
▴ 50
7
votes
20
replies
2.0k
views
Forum:
NGS RNA-Seq Analysis Pipeline Tophat vs STAR
STAR
RNA-Seq
TopHat
updated 10 months ago by
Ram
43k • written 3.2 years ago by
mikefeixu
▴ 10
12
votes
20
replies
2.2k
views
Is there a single header file somewhere I can use to read bam?
cpp
bam
c
updated 10 months ago by
Ram
43k • written 5.4 years ago by
Click downvote
▴ 720
12
votes
20
replies
1.1k
views
Help with gatk BaseRecalibrator
GATK
variant-calling
updated 3 months ago by
Ram
43k • written 3 months ago by
Chris
▴ 260
14
votes
20
replies
6.6k
views
7 follow
Tool Recommendations For Human Genome Assembly
assembly
human-genome
updated 9 months ago by
Ram
43k • written 11.1 years ago by
Chris Cole
▴ 800
28
votes
20
replies
21k
views
7 follow
how do I run repeat masker
repeatmasker
updated 10 weeks ago by
Andrzej Zielezinski
11k • written 8.3 years ago by
ksi216
▴ 80
12
votes
20
replies
2.3k
views
SEACR and MACS2
MACS2
SEACR
updated 9 months ago by
rfran010
▴ 900 • written 9 months ago by
qudrat.nii
▴ 10
49
votes
20
replies
1.9k
views
10 follow
Forum:
First experiences matter
first-time
tolerance
updated 11 weeks ago by
Michael Love
★ 2.6k • written 12 weeks ago by
Mensur Dlakic
★ 26k
83
votes
20
replies
19k
views
17 follow
How Do Pathway Databases Compare?
pathway
database
subjective
updated 8 months ago by
Peter Karp
▴ 30 • written 13.4 years ago by
Shigeta
▴ 470
0
votes
20
replies
1.5k
views
Rockhoppper - Suspiciously low percentage of perfectly aligned reads
Rockhopper
RNA-seq
5 months ago by
langziv
▴ 50
21
votes
20
replies
8.7k
views
11 follow
Laptops for bioinformatics
hardware
Laptops
updated 9 months ago by
LauferVA
4.1k • written 17 months ago by
tsomakiank
▴ 40
29
votes
20
replies
3.6k
views
Tool:
FastQt : a clone of FastQC in C++/Qt
fastqc
Cpp
fastq
Qt
updated 9 months ago by
Ram
43k • written 7.3 years ago by
sacha
★ 2.4k
22
votes
20
replies
2.5k
views
what is the prefered strategy to treat with blast-less transcriptomes from RNA-seq
blast
RNA-Seq
genome
gene
updated 11 months ago by
Ram
43k • written 7.7 years ago by
Farbod
★ 3.4k
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 4 months ago by
Ram
43k • written 14.0 years ago by
Scott
▴ 70
2
votes
20
replies
2.2k
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
6 months ago by
Maxine
▴ 40
37
votes
20
replies
7.1k
views
14 follow
Online Bioinformatics Resources
online-resources
updated 4 months ago by
Ram
43k • written 14.0 years ago by
Eric Normandeau
11k
22
votes
20
replies
4.7k
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 9 months ago by
Ram
43k • written 5.4 years ago by
Charlotte.Herzeel
▴ 150
9
votes
20
replies
2.6k
views
Bioinformatics Perl Help
Perl
updated 11 months ago by
Ram
43k • written 8.0 years ago by
ksi216
▴ 80
42
votes
20
replies
3.3k
views
11 follow
Forum:
What are the most popular NGS tools?
ensembl
NGS
updated 11 months ago by
Ram
43k • written 8.0 years ago by
Emily
23k
1
vote
20
replies
1.5k
views
randomreads.sh only produces reads for chr1 to chr7
randomreads.sh
bbmap
updated 8 months ago by
GenoMax
140k • written 9 months ago by
berndmann
▴ 10
17
votes
20
replies
1.3k
views
What is the best way to compute genetic distances between FASTQ files?
genetic-distance
fastq
updated 5 months ago by
GenoMax
140k • written 5 months ago by
mikazon
▴ 10
0
votes
20
replies
1.5k
views
How can I obtain the DNA sequences of each CDS for several genbank files?
genbank
DNA
sequence
3 months ago by
Raphaëlle
• 0
25
votes
19
replies
8.0k
views
10 follow
Tool:
pathfindR - Enrichment Analysis using Active Subnetworks
subnetwork
R
pathway-enrichment
updated 9 months ago by
Ram
43k • written 6.1 years ago by
egeulgen
★ 1.3k
15
votes
19
replies
8.6k
views
6 follow
Tool:
Gemini: Integrative Exploration Of Genetic Variation And Genome Annotations
vcf
database
genome
variation
updated 9 months ago by
Ram
43k • written 10.9 years ago by
Aaronquinlan
12k
93
votes
19
replies
59k
views
18 follow
What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
phylogenetics-tree
updated 9 months ago by
Ram
43k • written 13.6 years ago by
Niek De Klein
★ 2.6k
66
votes
19
replies
50k
views
17 follow
Tool To Find Out If Fastq Is In Sanger Or Phred64 Encoding?
fastq
updated 9 months ago by
Ram
43k • written 11.1 years ago by
14134125465346445
★ 3.6k
130
votes
19
replies
30k
views
9 follow
Could you explain the difference between STAR, KALLISTO, SALMON etc. to experimental Biologist/non-bioinformatician
RNA-Seq
alignment
next-gen
R
assembly
updated 9 weeks ago by
Ram
43k • written 4.5 years ago by
WUSCHEL
▴ 750
30
votes
19
replies
9.7k
views
6 follow
Forum:
Programming language use distribution from recent programs / articles
programming-language
programs
updated 10 months ago by
Ram
43k • written 6.9 years ago by
Eric Normandeau
11k
3
votes
19
replies
1.4k
views
Systematic errors at the end and beginning of reads in NGS panels
NGS
error
panels
sequencing
updated 8 months ago by
Asaf
10k • written 8 months ago by
captainlabman
▴ 20
20
votes
19
replies
4.1k
views
7 follow
Bioinformatics word cloud to use in classes
teaching
education
updated 10 months ago by
Ram
43k • written 5.1 years ago by
gramarga
▴ 50
7
votes
19
replies
3.3k
views
CUT&Tag data processing: peak caller choice and typical peak size profile
CUTandTag
MACS2
SEACR
ChIPseq
gopeaks
updated 10 months ago by
gglim
▴ 140 • written 15 months ago by
nihilior
▴ 50
38
votes
19
replies
11k
views
Tool:
Excel add-in for DNA/RNA string manipulations
sequence
DNA
RNA
Excel
updated 9 months ago by
Ram
43k • written 8.1 years ago by
jgbaum
▴ 140
34
votes
19
replies
47k
views
11 follow
Convert Refseq Id To Gene Name
refseq
gene
updated 8 months ago by
Ram
43k • written 10.8 years ago by
hicsuntdrac0nis
▴ 250
28
votes
19
replies
15k
views
10 follow
How To Generate Mutations In Sequences Of A Fasta File?
fasta
python
mutation
sequence
updated 9 months ago by
Ram
43k • written 12.5 years ago by
Geparada
★ 1.5k
12
votes
19
replies
14k
views
11 follow
SnpMatrix from VCF file
VCF
Eqtl
MatrixEQTL
SnpMatrix
vcftools
updated 14 days ago by
pmiller
▴ 10 • written 7.0 years ago by
Dhana
▴ 110
40
votes
19
replies
9.5k
views
12 follow
Is There A Site Where Call For Papers And Conferences Are Listed In One Place?
papers
conference
updated 4 months ago by
Ram
43k • written 14.0 years ago by
Brandstaetter
▴ 270
23
votes
19
replies
4.2k
views
7 follow
Tool:
Big Browser : a new genom browser in development
genome-browser
updated 9 months ago by
Ram
43k • written 8.1 years ago by
sacha
★ 2.4k
12
votes
19
replies
5.2k
views
how to identify CDR region in antibody sequence
CDR
antibody
updated 28 days ago by
tiancheng
• 0 • written 21 months ago by
reany
▴ 50
97
votes
19
replies
93k
views
12 follow
How To Get The Sequence Of A Genomic Region From Ucsc?
ucsc
fasta
sequence
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Giovanni M Dall'Olio
28k
6
votes
19
replies
9.9k
views
Translating DNA to protein with perl
perl
updated 11 months ago by
Ram
43k • written 8.0 years ago by
ksi216
▴ 80
56
votes
19
replies
4.0k
views
9 follow
Forum:
How to apply for a job
resume
cover-letter
application
CV
updated 10 months ago by
Ram
43k • written 6.7 years ago by
Emily
23k
1
vote
19
replies
775
views
Matching transcriptomic data to clinical data
R
updated 7 weeks ago by
Ram
43k • written 8 weeks ago by
Khadija
▴ 10
38
votes
19
replies
10k
views
10 follow
Forum:
Kallisto New RNA-seq quantification method discussion
RNA-Seq
updated 11 months ago by
Ram
43k • written 8.0 years ago by
morovatunc
▴ 550
3
votes
19
replies
1.1k
views
extract sequence from genome by region
fasta
updated 3 months ago by
Ram
43k • written 3 months ago by
gernophil
▴ 80
13
votes
19
replies
4.7k
views
Sum column until a certain value is reached then print that line
bedgraph
awk
updated 11 months ago by
Ram
43k • written 8.1 years ago by
josephmccarter1
▴ 80
45
votes
19
replies
2.8k
views
9 follow
Forum:
Where and how NGS techniques are heading for the next 5 years?
next-gen
NGS
updated 10 months ago by
Ram
43k • written 6.8 years ago by
lakhujanivijay
5.8k
75
votes
19
replies
3.3k
views
11 follow
Blog:
A list of technical advantages of Snakemake over Nextflow | Cloud solution for Snakemake
Snakemake
updated 27 days ago by
LauferVA
4.1k • written 6 months ago by
Kenny
▴ 30
23
votes
19
replies
6.8k
views
10 follow
Tutorial:
MutScan: Detect important mutations by scanning FastQ files directly
fastq
mutation
cancer
target
updated 11 months ago by
Ram
43k • written 7.5 years ago by
chen
★ 2.5k
5
votes
19
replies
3.9k
views
8 follow
Hisat2 aligner problem
RNA-Seq
ChIP-Seq
alignment
Assembly
software error
updated 3 months ago by
ATpoint
81k • written 4.9 years ago by
ta_awwad
▴ 340
0
votes
18
replies
1.7k
views
bcl2fastq conversion with specifying exact match of indices
genome
RNA-Seq
sequencing
updated 7 months ago by
GenoMax
140k • written 7 months ago by
Apex92
▴ 280
1,000 results • Page
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Comment: Gene reads all zero for each sample
Synthetic lethality and cancer database
Answer: log2(TPM+1)
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5.3k
That sounds fun, and I've got some of these that I have told many people about (to keep them from making the same mistakes as me). I am pla…
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for hgnc and ensembl that can be done for transcript id for human to mouse ortholog its difficult to parse and map the exact version from g…
Comment: Announcement: Research Topic "Mechanistic, Machine Learning and Hybrid Models of
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Take it from someone who has hosted both a successful and a failed research topic: these deadlines are unrealistic. I am guessing you are p…
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Awesome, years ago I wrote my thesis on the use of Tau to calculate tissue specificity, enjoy! The supplementary materials in the paper is…
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That error is on the server side, nothing to do with you, and is very common. Usually the fix is to try again in an hour, or to insert host…
Comment: Nanopore multisample variant calling
by
emilydolivo97
• 0
hello @colindaven , Did you find a suitable tool for this purpose please ? I'm dealing with fungal dataset
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Can you upload or post a link to the genbank file please?
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I usually perform biomaRt queries with their `getBM()` function where I list the input using `filter` and `values` option and my request in…
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• 0
Thank you for your response. I have often seen commands like dds <- estimateSizeFactors(dds) normalized_counts <- counts(dds, normalized=T…
Comment: Number of CPUs to use by DRAP for transcriptomic assmbly
by
Mohamed Abderrahmane
▴ 10
It's the case that there's no indication of multi-threading in the documentation. However, it made me wonder why the developers would restr…
Answer: Is RNAseq data from a monoclonal cell line technically considered scRNAseq?
by
Soheil
▴ 100
Bulk RNAseq from any sample is still considered a bulk sample. Running bulk RNA sequencing on a sample with any level of cell type/state c…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Yikes. Well, this is from an Illumina MiniSeq. Sure, I will use alignment, but only to remove host reads. Then the remaining reads will go …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
This is going to be tough to diagnose. Are you going to align to a reference? If so go ahead with the alignments to see if alignments turn …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
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BRENO
• 0
Thank you for replying. I have separated the reads with at least one N on them and they account for 0.2% of the total reads in the file (8'…
Comment: Error running local blastn in R using system2
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Mensur Dlakic
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The `-db data/nt_euk` switch means that in your current directory you have a subdirectory called `data`, and all the `nt_euk` files are in …
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