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1,000 results • Page
2 of 20
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Votes
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32
votes
51
replies
20k
views
8 follow
Getting Unmapped Reads: Comparing Fastq To Bam
fastq
samtools
bedtools
bam
updated 12.4 years ago by
brentp
24k • written 12.4 years ago by
User 9996
▴ 840
27
votes
50
replies
18k
views
7 follow
Extract fasta sequences from a large file using a list of names
fasta
updated 14 months ago by
Ram
43k • written 9.0 years ago by
fhsantanna
▴ 610
93
votes
50
replies
16k
views
17 follow
Forum:
Fda Sends A Warning Letter To 23Andme - Personal Genomics Service Marketing To Be Discontinued
personal-genomics
23andMe
updated 14 months ago by
Ram
43k • written 10.4 years ago by
Istvan Albert
100k
188
votes
50
replies
73k
views
41 follow
How To Remove The Same Sequences In The Fasta Files?
fasta
sequence
duplicates
updated 19 months ago by
Ram
43k • written 13.5 years ago by
Zhangleisdau
▴ 340
92
votes
50
replies
53k
views
16 follow
PCA plot from read count matrix from RNA-Seq
RNA-Seq
pca
updated 2.4 years ago by
BioNovice247
▴ 20 • written 6.5 years ago by
rachel.kubik12
▴ 220
12
votes
50
replies
4.1k
views
How can I find out the Linux version and what is the ftp command to install R and R Studio on Linux server?
R
7.1 years ago by
thomas.f.hahn2
▴ 100
26
votes
50
replies
14k
views
8 follow
Tool:
Retrieve a subset of FASTA from large Illumina multi-FASTA file
fasta
multi-fasta
illumina
updated 10 months ago by
Ram
43k • written 7.9 years ago by
hcwang
▴ 50
22
votes
50
replies
17k
views
Why I can not install anything on R?
R
software error
5.5 years ago by
Za
▴ 140
85
votes
49
replies
10k
views
31 follow
Which Application Is Truly Missing In Bioinformatics?
subjective
general
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Jarretinha
3.4k
262
votes
48
replies
23k
views
37 follow
Forum:
Bioinformatics courses, workshops or training
Workshop
Training
Courses
updated 14 months ago by
Lars
★ 1.0k • written 9.0 years ago by
Deepak Tanwar
★ 4.2k
39
votes
48
replies
7.0k
views
CUTADAPT in windows
sequencing
updated 14 months ago by
Ram
43k • written 9.0 years ago by
zizigolu
★ 4.3k
90
votes
48
replies
33k
views
29 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 5 months ago by
Ram
43k • written 10.5 years ago by
Irsan
★ 7.8k
72
votes
48
replies
18k
views
15 follow
Tutorial:
For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
ngs
alignment
bwa
updated 14 months ago by
Ram
43k • written 11.2 years ago by
lh3
33k
131
votes
48
replies
16k
views
19 follow
Justifying Learning Linux For Bioinformatics
linux
subjective
updated 12.7 years ago by
Guangchuang Yu
★ 2.6k • written 12.7 years ago by
Eric Normandeau
11k
68
votes
48
replies
8.7k
views
16 follow
Forum:
Stranger Things: unexpected limitations of popular tools
samtools
hisat2
updated 11 months ago by
Ram
43k • written 6.8 years ago by
Istvan Albert
100k
72
votes
48
replies
8.5k
views
18 follow
What Kind Of Bioinformatics Tutorials Would You Like To See Online?
education
updated 14 months ago by
Ram
43k • written 13.0 years ago by
User 59
13k
22
votes
47
replies
5.3k
views
(solved) I couldn't reproduce the problem of max_target_seqs
blast
updated 5.1 years ago by
gb
★ 2.2k • written 5.6 years ago by
fishgolden
▴ 510
18
votes
47
replies
4.7k
views
Fastq Trimmer by pattern
fastq
trimming
reads
terminal
7.2 years ago by
dzisis1986
▴ 70
23
votes
47
replies
7.1k
views
6 follow
Dbsnp Individual Genotyping Information For Specific Snps
dbsnp
updated 13.1 years ago by
Khader Shameer
18k • written 13.1 years ago by
Andrea_Bio
★ 2.8k
188
votes
47
replies
2.8k
views
16 follow
Job:
Bioinformatics freelancers needed
freelancer
updated 12 months ago by
Ram
43k • written 8.0 years ago by
Bioinfexperts
▴ 190
176
votes
46
replies
19k
views
26 follow
Forum:
Crac: Funny And/Or Weird Names For Bioinformatics Tools
humor
5 months ago by
Istvan Albert
100k
43
votes
46
replies
4.2k
views
taking sequences of a list of miRNAs
miRNA
mirbase
sequence
gene
updated 7.5 years ago by
Ram
43k • written 7.5 years ago by
zizigolu
★ 4.3k
105
votes
46
replies
13k
views
13 follow
Forum:
Why Does Biostar Cover Questions On Epigenetics, But Not Intelligent Design?
epigenetics
updated 14 months ago by
Ram
43k • written 10.7 years ago by
ugly.betty77
★ 1.1k
126
votes
46
replies
50k
views
21 follow
Forum:
Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
visualization
ChIP-Seq
homer
ngsplot
deeptools
updated 12 months ago by
Ram
43k • written 8.1 years ago by
Sinji
★ 3.2k
37
votes
46
replies
6.9k
views
12 follow
Quick Programming Challenge: How Do I Calculate Reference Coverage From A Table Of Alignment Starts And Ends?
code
alignment
programming
updated 5.6 years ago by
Ram
43k • written 14.0 years ago by
Jeremy Leipzig
22k
83
votes
46
replies
8.8k
views
15 follow
Tool:
ChatGPT optimized for bioinformatics questions
gpt
updated 6 weeks ago by
LauferVA
4.2k • written 10 months ago by
Sasha
▴ 840
92
votes
46
replies
12k
views
28 follow
Best Language For Introductory Programming Course From Within An Introduction Course On Bioinformatics.
programming
subjective
updated 14 months ago by
Ram
43k • written 12.8 years ago by
Andra Waagmeester
3.2k
4
votes
45
replies
7.7k
views
SAM file wrong? help with validatesamfile
EXOME
updated 12 months ago by
Ram
43k • written 7.8 years ago by
cristina_sabiers
▴ 110
237
votes
45
replies
72k
views
34 follow
What Is The Best Pipeline For Human Whole Exome Sequencing?
next-gen
sequencing
illumina
exome
human
updated 12.9 years ago by
User 9126
▴ 50 • written 13.9 years ago by
Biomed
5.0k
108
votes
45
replies
86k
views
30 follow
How To Extract A Sequence From A Big (6Gb) Multifasta File ?
fasta
updated 20 months ago by
aswinssoman
▴ 70 • written 11.8 years ago by
Mchimich
▴ 320
185
votes
45
replies
32k
views
27 follow
How To Organize A Pipeline Of Small Scripts Together?
pipeline
general
updated 6 months ago by
Ram
43k • written 14.2 years ago by
Giovanni M Dall'Olio
28k
22
votes
45
replies
13k
views
9 follow
Tool to separate human and mouse rna seq reads
RNA-Seq
next-gen-sequencing
updated 15 months ago by
Ram
43k • written 8.9 years ago by
Ron
★ 1.2k
27
votes
44
replies
15k
views
How to remove contamination from the transcriptome assembly
RNA-Seq
contamination
assembly
blast
Hiseq reads
updated 20 months ago by
Ram
43k • written 8.5 years ago by
seta
★ 1.9k
43
votes
44
replies
5.7k
views
14 follow
Macbook M1 pro/M2 pro or Dell (with Ubuntu/other linux distribution) for bioinformatics stuff?
metagenomics
amplicon
macbook
Intel
MacOs
updated 6 months ago by
steve
★ 3.5k • written 6 months ago by
l.gallucci
▴ 10
121
votes
44
replies
21k
views
21 follow
What Is Your Favorite Question To Ask When Interviewing Potential Bioinformaticians?
subjective
updated 14 months ago by
Ram
43k • written 13.9 years ago by
Madelaine Gogol
5.3k
196
votes
44
replies
72k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
microarray-analysis
bioconductor
updated 15 months ago by
Ram
43k • written 11.6 years ago by
Obi Griffith
20k
155
votes
44
replies
32k
views
29 follow
Which Bioinformatic Friendly Pipeline Building Framework?
scripting
updated 22 months ago by
Ram
43k • written 10.3 years ago by
Carlos Borroto
★ 2.1k
122
votes
44
replies
11k
views
24 follow
News:
Help Make Biostar Better! Add Your Feedback, Opinions And Suggestions.
meta
biostars
updated 6 months ago by
Ram
43k • written 11.4 years ago by
Istvan Albert
100k
46
votes
44
replies
25k
views
9 follow
bash loop for alignment RNA-seq data
RNA-Seq
next-gen
alignment
updated 19 months ago by
Ram
43k • written 10.0 years ago by
Paul
★ 1.5k
99
votes
44
replies
24k
views
33 follow
Best Free Text Editor For All Popular Languages (R, Python, Perl Etc..)
text
r
perl
python
updated 6.6 years ago by
grant.hovhannisyan
★ 2.6k • written 12.1 years ago by
John
★ 1.5k
102
votes
44
replies
9.1k
views
22 follow
What Are Numbers Every Bioinformatician Should Know?
knowledge
career
updated 14 months ago by
Ram
43k • written 10.7 years ago by
brentp
24k
21
votes
44
replies
4.3k
views
How to analyze Illumina RNASeq data
RNA-Seq
sequencing
next-gen
3.7 years ago by
Kumar
▴ 170
130
votes
44
replies
34k
views
16 follow
Forum:
Trimming adapter sequences - is it necessary?
NGS
adapter
RNA-Seq
updated 13 months ago by
Ram
43k • written 7.6 years ago by
Lars
★ 1.0k
90
votes
44
replies
60k
views
28 follow
Tool to generate proportional Venn Diagrams?
visualization
updated 2.0 years ago by
Ram
43k • written 13.0 years ago by
Ryan D
★ 3.4k
185
votes
44
replies
83k
views
30 follow
Drawing Chromosome Ideograms With Data
ideogram
visualization
chromosome
updated 5 weeks ago by
Michael
54k • written 14.1 years ago by
Yuri
★ 1.7k
1
vote
43
replies
4.0k
views
Database from .gbk files
database
gbk
ncbi
updated 12 months ago by
Raul
• 0 • written 3.9 years ago by
graysonford
▴ 10
16
votes
43
replies
6.7k
views
Stuck on calculating principal components
Vegan
R
software error
SNP
updated 6.4 years ago by
pfs
▴ 280 • written 6.4 years ago by
zizigolu
★ 4.3k
66
votes
43
replies
27k
views
23 follow
Ngs - Huge (Fastq) File Parsing - Which Language For Good Efficiency ?
next-gen
sequencing
parsing
fastq
programming
updated 2.2 years ago by
Ram
43k • written 13.3 years ago by
toni
★ 2.2k
31
votes
43
replies
19k
views
11 follow
Volcano plot help code
R
rna-seq
updated 5.8 years ago by
jordi.planells
▴ 480 • written 6.0 years ago by
anasofiamoreira94
▴ 80
59
votes
43
replies
21k
views
18 follow
Tutorial:
Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
pbalign
pacbio
arrow
smrt-limk
updated 13 months ago by
Ram
43k • written 6.6 years ago by
Rox
★ 1.4k
1,000 results • Page
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Recent Votes
biomaRt external_gene_name same entry multiple times when mapping to homolog mouse gene
Converting between Ensembl Versions
Comment: what is the purpose of indexing the reference genome (Kallisto)
Answer: what is the purpose of indexing the reference genome (Kallisto)
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
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Comment: genome assembly records not present in assembly_summary.txt
by
GenoMax
141k
Can you clarify what `metainfo` you are referring to? The accession that you refer to does exist in [**GenBank assembly_summary file**][1…
Comment: what is the purpose of indexing the reference genome (Kallisto)
by
i.sudbery
19k
Specifically: If we want to look up all the places where a 31mer is in a genome without and index, we have to compare that 31 to the first…
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
benformatics
3.9k
This is way easier to do solely in R now 10 years later. library(GenomicFeatures) library(rtracklayer) ## import GTF…
Answer: what is the purpose of indexing the reference genome (Kallisto)
by
dsull
★ 5.8k
I'll see if I can explain things in super simple terms (albeit with some abuse of the actual technical details) to provide a conceptual und…
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
Jalil Sharif
▴ 80
The updated code in R using rtracklayer for reading a gtf file. https://github.com/jalilsharif/gtf_utr_fix_r/blob/main/gencode_utr_fix_d…
Comment: Rare Disease Variant Pathway Analysis
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▴ 10
Thank you LauferVA, Your advice has been useful and I now a lot to think about and read. Also, I just wanted to clarify I do not ha…
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by
Antonio R. Franco
★ 5.1k
You cannot do it with Kallisto either. In fact, the indexation will fail in attempting to index a genome file
Comment: PCA plot
by
ATpoint
82k
What is your question? Add details and clarity. Ask a precise question and please avoid opening more questions on the same underlying issue…
Comment: genome assembly records not present in assembly_summary.txt
by
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21k
If you have the accession numbers can you not use something like `eutils`?
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Pierre Lindenbaum
161k
> Next, I tried using bedtools window but in your original post you said > tried finding the intersection of these bed files using bedto…
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by
Lada
▴ 30
Thank you very much! I tried it out! This is a handy tool useful for many different applications, and in regards to my problem - although …
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
• 0
Thank you for replying Pierre. I first added a third column to the SNP bed file, so that I would get a range of 1 for each SNP awk 'B…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
Pierre Lindenbaum
161k
> using bcftools Show us what you tried
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Thank you for replying here; this helped me figure out why MAPK10 was missing from my results. It was also marked as a pseudogene in the En…
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