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1,000 results • Page
2 of 20
Sort: Votes
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Views
Votes
Replies
149
votes
35
replies
62k
views
33 follow
Tutorial:
Tools For Metagenomic Data Analysis
metagenomics
next-gen
updated 14 months ago by
Ram
43k • written 11.4 years ago by
vijay
★ 1.6k
149
votes
70
replies
50k
views
20 follow
Tutorial:
Network plot from expression data in R using igraph
microarray
RNA-Seq
R
network
updated 8 months ago by
Raheleh
▴ 260 • written 6.4 years ago by
Kevin Blighe
87k
147
votes
13
replies
25k
views
Alignment and mapping
alignment
next-gen
mapping
updated 8.2 years ago by
Benn
8.3k • written 8.2 years ago by
statfa
▴ 760
147
votes
34
replies
55k
views
17 follow
Tutorial:
Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music
cancer
tcga
mutation
maf
updated 14 months ago by
Ram
43k • written 11.0 years ago by
Cyriac Kandoth
6.0k
147
votes
31
replies
138k
views
26 follow
Useful Bash Commands To Handle Fasta Files
command-line
fasta
bash
updated 9 months ago by
Ram
43k • written 12.2 years ago by
Anima Mundi
★ 2.9k
145
votes
56
replies
8.9k
views
17 follow
Forum:
Suggesting The Removal Of Post Closing
biostars
updated 14 months ago by
Ram
43k • written 11.1 years ago by
Istvan Albert
100k
144
votes
62
replies
12k
views
23 follow
Forum:
Is The Biostar Fading? (Updated For 2014)
meta
biostars
updated 14 months ago by
Ram
43k • written 13.2 years ago by
Joachim
★ 2.9k
144
votes
14
replies
22k
views
15 follow
What Are The Classic Papers In Bioinformatics?
literature
papers
history
updated 3.1 years ago by
Jeremy Leipzig
22k • written 13.5 years ago by
Casey Bergman
18k
143
votes
14
replies
169k
views
16 follow
What Is The Sequencing 'Depth' ?
next-gen
sequencing
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Pierre Lindenbaum
161k
143
votes
33
replies
30k
views
20 follow
C/C++ Libraries For Bioinformatics?
c
c
updated 5.1 years ago by
chernouhov sergey
▴ 50 • written 13.9 years ago by
User 59
13k
142
votes
21
replies
30k
views
12 follow
Tutorial:
A few words for R beginners
Swirl
R
updated 24 months ago by
Ram
43k • written 9.4 years ago by
Parham
★ 1.6k
139
votes
25
replies
84k
views
14 follow
Tutorial:
Piping With Samtools, Bwa And Bedtools
unix
samtools
bwa
bedtools
updated 2.1 years ago by
Ram
43k • written 12.0 years ago by
Ying W
★ 4.2k
138
votes
42
replies
22k
views
22 follow
Forum:
Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
meta
updated 13 months ago by
LauferVA
4.2k • written 10.9 years ago by
Whetting
★ 1.6k
138
votes
22
replies
66k
views
15 follow
How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental Biologist/non-bioinformatician
gene
LIMMA
edgeR
updated 11 months ago by
Kevin Blighe
87k • written 6.5 years ago by
Mike
★ 1.9k
138
votes
33
replies
66k
views
19 follow
VCF files: Change Chromosome Notation
vcf
next-gen
sequence
updated 18 months ago by
Ram
43k • written 10.0 years ago by
Quak
▴ 490
138
votes
21
replies
71k
views
18 follow
Database Of Tumor Suppressors And/Or Oncogenes
cancer
gene
database
oncogene
tumor
3.6 years ago by
Malachi Griffith
19k
136
votes
29
replies
7.6k
views
16 follow
How Do We Discourage Ad-Hoc Bioinformatic Analyses?
software
updated 2.0 years ago by
Ram
43k • written 13.3 years ago by
Jeremy Leipzig
22k
136
votes
26
replies
25k
views
14 follow
Best Way For A Beginner To Get Up To Speed On Unix Quickly?
unix
perl
genomics
updated 14 months ago by
Ram
43k • written 12.3 years ago by
Brett Thomas
▴ 300
135
votes
18
replies
170k
views
16 follow
Blast - Formatting Output
blast
format
output
updated 16 months ago by
katieostrouchov
▴ 30 • written 10.4 years ago by
timjoncooper
▴ 320
134
votes
65
replies
6.1k
views
11 follow
Forum:
Bioinformatics vs. the Climate Crisis
RNA-Seq
Climate
updated 11 months ago by
Ram
43k • written 4.4 years ago by
sviatoslav.kendall
▴ 880
134
votes
27
replies
45k
views
14 follow
Why Are There Many Rna-Seq Hits To Intronic Regions?
rna-seq
updated 2.0 years ago by
Ram
43k • written 12.0 years ago by
lh3
33k
133
votes
123
replies
38k
views
23 follow
Tutorial:
Survival analysis with gene expression
cox
gene-expression
survival-analysis
geo
updated 13 months ago by
1769mkc
★ 1.2k • written 5.5 years ago by
Kevin Blighe
87k
131
votes
19
replies
183k
views
13 follow
What'S The Difference Between Cds And Orf?
cds
orf
updated 3.0 years ago by
kajumi
• 0 • written 11.9 years ago by
shiy05
▴ 370
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
130
votes
19
replies
31k
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 3 months ago by
Ram
43k • written 4.6 years ago by
WUSCHEL
▴ 750
130
votes
44
replies
34k
views
16 follow
Forum:
Trimming adapter sequences - is it necessary?
NGS
adapter
RNA-Seq
updated 14 months ago by
Ram
43k • written 7.6 years ago by
Lars
★ 1.0k
130
votes
37
replies
14k
views
27 follow
What Are The Obsolete Research Topics In Bioinformatics?
updated 12.7 years ago by
Pals
★ 1.3k • written 12.7 years ago by
Sirus
▴ 820
129
votes
38
replies
8.3k
views
21 follow
Forum:
Who are the Greatest Bioinformaticians Of All Time (GBOAT)
bioinformatics
updated 11 months ago by
Ram
43k • written 5.1 years ago by
Istvan Albert
100k
129
votes
32
replies
129k
views
29 follow
Is There A Free Alternative To Ingenuity Pathway Analysis?
network
pathway
updated 2.1 years ago by
Ram
43k • written 13.2 years ago by
Gon
▴ 540
128
votes
83
replies
13k
views
8 follow
Tool:
Lossless ALAPY Fastq Compressor (now for MacOS X with 10-20% improved speed and compression ratio)
lossless-fastq-compression
fastq-compressor
updated 10 months ago by
Ram
43k • written 7.1 years ago by
Petr Ponomarenko
★ 2.8k
128
votes
24
replies
85k
views
18 follow
Sequence Length Distribution From A Fastq File
sequence
length
fastq
updated 5.0 years ago by
LuckyLuck
• 0 • written 11.0 years ago by
deepthithomaskannan
▴ 380
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 13 months ago by
Ram
43k • written 8.2 years ago by
Sinji
★ 3.2k
124
votes
56
replies
103k
views
24 follow
How to plot coverage and depth statistics of a bam file
bam
coverage
depth
next-gen-sequencing
updated 7 months ago by
William
▴ 30 • written 9.9 years ago by
kay
▴ 370
124
votes
13
replies
174k
views
13 follow
How Can I Convert Bam To Sam?
bam
next-gen-sequencing
sam
updated 8 months ago by
Ram
43k • written 13.8 years ago by
Biomed
5.0k
124
votes
29
replies
7.3k
views
18 follow
What License Do You Use When You Release Code And Data?
software
general
subjective
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Simon Cockell
7.4k
122
votes
17
replies
76k
views
8 follow
What Are Phased And Unphased Genotypes?
genotyping
genome
updated 2.1 years ago by
Ram
43k • written 13.0 years ago by
Nick
▴ 370
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
121
votes
29
replies
36k
views
11 follow
PCA in a RNA seq analysis
RNA-Seq
pca
updated 5.4 years ago by
Giovanni M Dall'Olio
28k • written 6.5 years ago by
Mozart
▴ 330
121
votes
7
replies
118k
views
Bam And Indexed Bam Files
bam
index
12.3 years ago by
Sahel
▴ 260
121
votes
33
replies
39k
views
24 follow
Forum:
Where To Look For Quality Bioinformatics Short Courses And Workshops?
Courses
updated 11 months ago by
carlopecoraro2
★ 2.5k • written 10.7 years ago by
Eric Normandeau
11k
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
121
votes
35
replies
43k
views
20 follow
Forum:
Snakemake vs. Nextflow: strengths and weaknesses
snakemake
nextflow
updated 11 months ago by
Ram
43k • written 6.9 years ago by
ropolocan
▴ 810
120
votes
23
replies
31k
views
14 follow
Why are we still using Bam files? And not Cram, HDF5 or improved Bam files?
cram
bam
io
hdf
updated 3.1 years ago by
Ram
43k • written 9.8 years ago by
WilliamS
▴ 320
120
votes
31
replies
199k
views
17 follow
Correct Way To Parse A Fasta File In Python
python
fasta
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Eric Normandeau
11k
120
votes
8
replies
80k
views
GRCh37/38(NCBI) vs hg19/hg38(UCSC)
ncbi
ucsc
grch38
hg38
updated 2.3 years ago by
Ram
43k • written 9.6 years ago by
pwg46
▴ 540
119
votes
25
replies
123k
views
12 follow
Where Can I Download Human Reference Genome In Fasta Format? Hgref.Fa File
human
fasta
sequence
bwa
updated 7.2 years ago by
Hajk-Georg Drost
▴ 160 • written 13.8 years ago by
Biomed
5.0k
118
votes
15
replies
105k
views
15 follow
Economics Of A Career In Bioinformatics
career
updated 13.3 years ago by
Mona Mohamed
• 0 • written 13.5 years ago by
Terence
▴ 210
118
votes
26
replies
36k
views
22 follow
Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
DESeq
Kallisto
RNASeq
Salmon
DESeq2
updated 13 months ago by
e.r.zakiev
▴ 210 • written 9.0 years ago by
mhockin
▴ 610
118
votes
74
replies
46k
views
40 follow
Is there a Lims that doesn't suck?
LIMS
updated 18 months ago by
GenoMax
142k • written 13.4 years ago by
Casbon
★ 3.3k
117
votes
66
replies
46k
views
20 follow
Tutorial:
[Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera
fastq-dump
Fastq
ENA
updated 13 months ago by
Ram
43k • written 5.8 years ago by
ATpoint
82k
1,000 results • Page
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Recent Votes
Answer: Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
How to convert plink data from 38th assembly to 37
How to convert plink data from 38th assembly to 37
Comment: How to access TCGA samples that were treated with a specific drug?
Comment: Normalize scRNAseq data to housekeeping genes to compare several datasets
Comment: Converting CRAM to FastQ
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Comment: How to access TCGA samples that were treated with a specific drug?
by
GenoMax
142k
It is possible that these drugs may not have been directly used in TCGA. Authors could have looked for mutations known to be acted on by th…
Comment: Does comparing two different groups to a common third group introduce bias in th
by
Qroid
▴ 40
Are you thinking about a specific scenario? If so, can you provide more info? I think the basic answer is that, yes, your choice of group C…
Answer: Bedtools merge minimum overlap?
by
harold.smith.tarheel
★ 4.9k
Bedtools [intersect][1] allows you to specify the fraction of overlap between two BED (or BAM) files using the F/f/r flags. You could split…
Comment: How to access TCGA samples that were treated with a specific drug?
by
Qroid
▴ 40
Sorry, I should have been more specific. By "that list" I mean what's populated in the Therapeutic Agents tab when no filters are applied. …
Comment: Bedtools merge minimum overlap?
by
bk11
★ 2.4k
Not sure if you wanting to do like this- cat your_input.bed chr1 100 200 region1 + chr1 180 300 regi…
Comment: Extract gRNA sequence using cutadapt
by
GenoMax
142k
If you know what the boundaries of your construct look like then trim the left-end of the read using the tag on that end (`ktrim=l`). Then …
Comment: Extract gRNA sequence using cutadapt
by
gernophil
▴ 80
> Not every read in your data is going to match a guide. That is also true for sure. Let me clarify what I mean. For every read you should…
Answer: VG : No reference-sense paths available in the graph; falling back to generic pa
by
anovak
▴ 120
If your GFA has paths in it that are P lines with names that don't include a sample name, contig name, and separators, then those are what …
Comment: Extract gRNA sequence using cutadapt
by
GenoMax
142k
> if you look at a fastq file you should be able to tell for every read definitely, if it has a perfect match for a guide in it and what gu…
Answer: DiffBind: no peaks in DBA
by
jared.andrews07
★ 16k
Because `dba.analyze` is not meant to be run directly on a peaks file. Have you read the documentation? In addition, a ChIP-seq experiment…
Comment: Converting CRAM to FastQ
by
Maverick
▴ 10
Thank you so much! Will look it up right away.
Comment: Extract gRNA sequence using cutadapt
by
gernophil
▴ 80
> I don't think every guide is supposed to show up in these experiments as far as I have seen. You will get some guides with 0 counts as yo…
Comment: Converting CRAM to FastQ
by
GenoMax
142k
Use `samtools view ` for this conversion. See discussion in https://www.biostars.org/p/9592860/ Specifically @jkbonfield's comment here --…
Comment: How to access TCGA samples that were treated with a specific drug?
by
GenoMax
142k
No that was only from Breast cancer. You could try selecting all data and see if you are able to see all treatments in the set. No idea a…
Comment: Extract gRNA sequence using cutadapt
by
GenoMax
142k
I don't think every guide is supposed to show up in these experiments as far as I have seen. You will get some guides with 0 counts as you …
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