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Limit : this month
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1,000 results • Page
2 of 20
Sort: Votes
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Views
Votes
Replies
23
votes
41
replies
2.5k
views
6 follow
I want to correct the erroneous barcode file, and the Python code that I've written, using Biopython, is very slow. How can I make this process fast…
NGS
biopython
illumina
WGS
updated 19 days ago by
Ram
39k • written 5 weeks ago by
Vijith
▴ 30
23
votes
15
replies
4.2k
views
6 follow
Forum:
On the usage of Golang
assembly
next-gen
alignment
updated 4 days ago by
Ram
39k • written 4.6 years ago by
Lucas Peres
▴ 80
23
votes
10
replies
2.4k
views
10 follow
Any suggestions for basic intro to submitting jobs to an HPC cluster?
ngs
hpc
updated 4 days ago by
Ram
39k • written 4.7 years ago by
m98
▴ 400
22
votes
11
replies
2.6k
views
Forum:
ExpressionSet in the age of tidyverse
expressionset
R
bioconductor
updated 6 days ago by
Ram
39k • written 5.1 years ago by
igor
13k
22
votes
15
replies
6.9k
views
11 follow
Forum:
RNASeq user experience with Novogene?
RNA-Seq
updated 5 days ago by
Ram
39k • written 4.9 years ago by
ivanarg2
▴ 80
22
votes
9
replies
17k
views
8 follow
Download Geo Tar File Automatically From Linux/Unix
unix
geo
updated 24 days ago by
zhupei1355974677
▴ 10 • written 10.4 years ago by
dfernan
▴ 730
21
votes
11
replies
1.6k
views
Forum:
Most important International Big Data Projects: Genetics and Epigenetics
big-data
updated 5 days ago by
Ram
39k • written 4.8 years ago by
Shicheng Guo
★ 9.3k
21
votes
7
replies
13k
views
Use samtools index on multiple bam files at the same time from the command line?
RNA-Seq
next-gen
sequence
updated 22 days ago by
Pierre Lindenbaum
154k • written 7.4 years ago by
nash.claire
▴ 470
21
votes
11
replies
1.6k
views
8 follow
Forum:
what I want to do after the PhD?
PhD
updated 18 days ago by
Ram
39k • written 6.2 years ago by
fi1d18
★ 4.2k
20
votes
2
replies
7.1k
views
Tutorial:
Creating a karyotype plot with genes using karyoploteR
karyoploteR
visualization
R
genome
updated 11 days ago by
Ram
39k • written 5.5 years ago by
bernatgel
★ 3.4k
20
votes
6
replies
4.2k
views
Some clarification on enrichment analyses and pathway analyses?
pathview
R
gene-enrichment
RNA-Seq
updated 11 days ago by
Ram
39k • written 5.5 years ago by
kirannbishwa01
★ 1.5k
20
votes
9
replies
30k
views
8 follow
Biomart Bioconductor - Retrieving All Entrezgenes Of Hsapiens_Gene_Ensembl
biomart
r
bioconductor
updated 22 days ago by
Kevin Blighe
85k • written 10.9 years ago by
sthait
▴ 120
20
votes
7
replies
2.8k
views
k-mer counting into R using perfect hashing
k-mer
Rcpp
Cpp
hashing
R
updated 7 days ago by
Ram
39k • written 6.9 years ago by
Macherki M E
▴ 120
20
votes
5
replies
8.2k
views
GATK_HaplotypeCaller: <NON_REF> .
GATK
updated 24 days ago by
Moe
▴ 10 • written 8.3 years ago by
iraun
6.0k
20
votes
24
replies
6.0k
views
6 follow
Forum:
Python or R
RNA-Seq
alignment
next-gen-sequencing
updated 6 days ago by
Ram
39k • written 5.0 years ago by
Qingyang Xiao
▴ 160
20
votes
19
replies
3.1k
views
7 follow
Bioinformatics word cloud to use in classes
teaching
education
updated 3 days ago by
Ram
39k • written 4.3 years ago by
gramarga
▴ 50
19
votes
9
replies
3.1k
views
Forum:
How to self-study (get onto) Bioinformatics and Data Analysis for Genomic, for working with real life genomics data?
R
genome
RNA-Seq
Python
updated 5 days ago by
Ram
39k • written 4.8 years ago by
WUSCHEL
▴ 720
19
votes
2
replies
3.1k
views
Tutorial:
Beginner's Handbook to Next Generation Sequencing
NGS
updated 17 days ago by
Ram
39k • written 6.1 years ago by
support
▴ 640
19
votes
15
replies
1.3k
views
6 follow
Forum:
Cross out line in Biostars
meta
updated 6 days ago by
Ram
39k • written 5.0 years ago by
Bastien Hervé
5.2k
19
votes
6
replies
3.1k
views
Forum:
ngs vs microarray
microarray
ngs
updated 5 days ago by
Ram
39k • written 4.9 years ago by
au.rinki.bio
▴ 20
19
votes
9
replies
27k
views
7 follow
Can anyone suggest a good tutorial to learn RNA-seq analysis?
analysis
RNA-Seq
ngs
updated 12 days ago by
Ram
39k • written 5.6 years ago by
Arindam Ghosh
▴ 480
18
votes
4
replies
2.5k
views
Paternity Testing from WGS Trio
WGS
trio
paternity test
DNA-Seq
updated 13 days ago by
geocarvalho
▴ 330 • written 4.7 years ago by
ClkElf
▴ 50
18
votes
2
replies
5.5k
views
Tutorial:
Update kraken databases
database
kraken
k-mer
python
updated 17 days ago by
Ram
39k • written 6.1 years ago by
Sej Modha
5.2k
18
votes
11
replies
1.9k
views
8 follow
Forum:
Create a File format to store Variant
hgvs
json
variant
updated 5 days ago by
Ram
39k • written 4.9 years ago by
sacha
★ 2.4k
18
votes
2
replies
2.9k
views
Forum:
Scripts on the Web: Bioinformatics Recipes
bioinformatics
updated 7 days ago by
Ram
39k • written 5.2 years ago by
Istvan Albert
98k
18
votes
7
replies
3.8k
views
Forum:
Review of the CIGAR string format
alignment
updated 4 days ago by
Ram
39k • written 4.6 years ago by
Juke34
7.9k
18
votes
16
replies
1.4k
views
Forum:
Why are people not working on gene prioritization and candidate gene selection for new experiment design?
gene-prioritization
updated 4 days ago by
Ram
39k • written 4.7 years ago by
prasadhendre
▴ 20
18
votes
6
replies
6.5k
views
VCF header line counting
vcf
header
updated 3 days ago by
beausoleilmo
▴ 530 • written 8.3 years ago by
basalganglia
▴ 40
18
votes
3
replies
5.4k
views
How to process (seems) Agilent microarrry data?
microarray
rna
updated 2 days ago by
survive
• 0 • written 3.9 years ago by
MatthewP
★ 1.2k
18
votes
9
replies
2.9k
views
6 follow
Job:
Seeking private tutor to learn RNA/ChIP-Seq data analysis
RNA-Seq
ChIP-Seq
updated 17 days ago by
Ram
39k • written 6.1 years ago by
syrez
▴ 40
18
votes
39
replies
3.0k
views
Tool:
CBioInfCpp.h as a C++ lib containing some functions for bioinformatics
cpp
updated 7 days ago by
Ram
39k • written 4.1 years ago by
chernouhov sergey
▴ 50
18
votes
12
replies
2.0k
views
6 follow
Forum:
why GATK makes things more complicated ?
genomics
updated 3 days ago by
Ram
39k • written 4.3 years ago by
Learner
▴ 260
18
votes
9
replies
3.0k
views
MAPQ filtering for clinical applications
MAPQ
clinical NGS
updated 5 days ago by
dunia.aburizeg
▴ 40 • written 5.7 years ago by
Kevin Blighe
85k
17
votes
13
replies
1.7k
views
Tutorial:
Screen shots of text (please don't)!
meta
updated 18 days ago by
Ram
39k • written 6.2 years ago by
Michael
52k
17
votes
17
replies
1.5k
views
6 follow
Forum:
Journal for beginners
journal
updated 7 days ago by
Ram
39k • written 5.2 years ago by
heref
▴ 20
17
votes
14
replies
1.5k
views
10 follow
Forum:
What would be the trend in next few years in NGS era?
NGS
sequencing
updated 3 days ago by
Ram
39k • written 4.5 years ago by
ahmad mousavi
▴ 750
16
votes
10
replies
15k
views
Regarding Split reads and discordant reads
genome
sequence
sequencing
alignment
updated 12 days ago by
Ram
39k • written 5.6 years ago by
DL
▴ 40
16
votes
9
replies
9.7k
views
6 follow
problems with MAF for MutSigCV (vcf2maf)
vcf2maf
snp
vcf
MutSigCV
gatk
updated 13 hours ago by
RAJDEEP
• 0 • written 8.8 years ago by
A. Domingues
★ 2.6k
16
votes
14
replies
2.6k
views
7 follow
Suggestions regarding bioinformatics journal
journal
updated 11 days ago by
Ram
39k • written 5.4 years ago by
pixie@bioinfo
★ 1.5k
16
votes
6
replies
6.9k
views
7 follow
Forum:
What computer skills should I put on my resume?
resume
genome
updated 11 days ago by
Ram
39k • written 5.5 years ago by
Kenny
▴ 30
16
votes
11
replies
3.2k
views
How to find out total # of CpGs sites from a fasta file?
sequence
Cpp
fasta
CpG
updated 7 days ago by
Ram
39k • written 6.5 years ago by
orlando.wong
▴ 60
16
votes
7
replies
1.0k
views
Forum:
What counts as "complex code"?
career
updated 4 days ago by
Ram
39k • written 4.8 years ago by
chrispyatt25
▴ 30
15
votes
6
replies
3.5k
views
Forum:
Which database software is better for bioinformatics web development? MySQL or MongoDB?
database
mysql
mongodb
software
updated 4 days ago by
Ram
39k • written 4.7 years ago by
mcclintock
▴ 10
15
votes
9
replies
1.7k
views
6 follow
Forum:
[Opinion] - What alignment software do you use?
next-gen
alignment
updated 7 days ago by
Ram
39k • written 5.2 years ago by
Andrew_MacGregor
▴ 30
15
votes
1
reply
6.4k
views
Tutorial:
A compilation of conversion tools for BED, SAM/BAM, psl, pslx, blast tabular and blast xml
psl
SAM
blast
BED
updated 11 days ago by
Ram
39k • written 5.5 years ago by
Joseph Hughes
★ 3.0k
15
votes
7
replies
17k
views
using featureCounts in command line
featureCounts
updated 25 days ago by
Adyasha
• 0 • written 7.7 years ago by
fi1d18
★ 4.2k
15
votes
10
replies
1.9k
views
6 follow
Forum:
help identifying bioinformatics operations tools
database
next-gen
operations
genomics
updated 3 days ago by
Ram
39k • written 4.5 years ago by
jsmedmar
▴ 80
15
votes
24
replies
1.9k
views
7 follow
Forum:
Airport.bio: First class ticket to any biological database in the world
RNA-Seq
ChIP-Seq
SNP
updated 7 days ago by
Ram
39k • written 5.1 years ago by
Bohdan Khomtchouk
▴ 350
15
votes
11
replies
3.7k
views
9 follow
Forum:
Methodological problems are extremely common for enrichment analysis - beware the pitfalls before you publish
GSEA
DAVID
enrichment-analysis
-geneontology
updated 10 days ago by
Ram
39k • written 14 months ago by
mark.ziemann
★ 1.8k
14
votes
6
replies
2.2k
views
6 follow
Forum:
Bioinformatics experience in programming
python
R
updated 4 days ago by
Ram
39k • written 4.7 years ago by
lucas_
▴ 20
1,000 results • Page
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Recent Votes
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Answer: What is the best way to clean bulk RNA-seq data?
What does <*> mean in a vcf file?
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Comment: Using entrez-direct inside a for loop in bash
by
GenoMax
129k
While your questions is unrelated to the original thread you should do the following (one PMID per line in input file): $ for i in `ca…
Comment: Using entrez-direct inside a for loop in bash
by
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• 0
Hi! I tried to do something similar, but it doesn't work. I have a list of Pubmed IDs and I want to retrieve their abstracts. for i …
Comment: featureCounts: ERROR: failed to find the gene identifier attribute
by
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yes I provided the column names just for showing it was a gtf file. Thanks for the recommendation of the SAF file. It worked!
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For the sake of simplicity and because it well stood the test of time I always use use `edgeR::filterByExpr()` which has reasonable default…
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Generally, you could use `bedops --chop` with some piping and process substitutions with `bedmap` to get count/ID/score data: bedops -…
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Hi, Thanks alot, This was really helpful and worked, however, I am looking for references where I can find how the minimap assign the MAPQ …
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swbarnes2
13k
You could still trick cellranger into processing them. Use umi tools to determine what the cell barcodes really are, (and see if they make…
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swbarnes2
13k
Well, A is a real letter. I don't know off the top of my head how cellranger deals with N's. But if the cell barcodes didn't match the v2 …
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by
David
• 0
That's the question, I think these data are not a useful entry for cellranger. Do you know if there is any other compatible software for th…
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David
• 0
I tried to add an "N" to the end of every read in R1 and cellranger did not found any barcode, results but no cells, I did it again adding …
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You can use Kmergenie (http://kmergenie.bx.psu.edu/). It is a special tool for finding the optimal k-mer length.
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It is pretty trivial to do the COSMIC annotation without tools such as VEP - download their coding and non-coding VCFs, normalize (decompos…
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Figured I need to attach an expected OUTPUT result. Should look something like this: ---------- ``` LOCUS 19 58617616 bp DNA HTG 23-NOV-2…
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Yes, well... surely it's better with some FPs and TPs than nothing at all, eh. Is there another way to do this? Hmm...
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