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120,713 results • Page
1 of 2415
Sort: Views
Rank
Views
Votes
Replies
66
votes
3
replies
312k
views
Understanding up and down regulated genes from LOG2 foldchange or foldchange
protein
gene-expression
RNA-Seq
updated 2.0 years ago by
Ram
45k • written 10.8 years ago by
Whoknows
▴ 960
283
votes
29
replies
304k
views
25 follow
How To Filter Mapped Reads With Samtools
samtools
updated 2.3 years ago by
Ram
45k • written 12.4 years ago by
sohadb1357
▴ 640
227
votes
39
replies
292k
views
33 follow
Gene Id Conversion Tool
david
updated 17 months ago by
Ram
45k • written 15.4 years ago by
Renee
▴ 620
347
votes
94
replies
258k
views
59 follow
Tools To Calculate Average Coverage For A Bam File?
coverage
bam
sequencing
updated 7 months ago by
GenoMax
149k • written 14.1 years ago by
Biomed
5.0k
122
votes
31
replies
214k
views
17 follow
Correct Way To Parse A Fasta File In Python
python
fasta
updated 16 months ago by
Ram
45k • written 14.9 years ago by
Eric Normandeau
11k
12
votes
6
replies
211k
views
How can I uninstall my packages in Rstudio
R
Bioconductor
updated 4.5 years ago by
zx8754
12k • written 7.1 years ago by
hassanlou110
▴ 40
43
votes
24
replies
209k
views
25 follow
How To Update R In Ubuntu ?
r
ubuntu
updated 2.9 years ago by
matthew.pace
▴ 60 • written 11.3 years ago by
Arpitha Hebbar
▴ 210
62
votes
14
replies
202k
views
9 follow
How To Deal With Duplicate Row Names Error In R
r
updated 23 months ago by
zx8754
12k • written 12.1 years ago by
Diana
▴ 930
168
votes
8
replies
198k
views
Generate vcf.gz file and its index file vcf.gz.tbi
vcf
tabix
updated 2.7 years ago by
Ram
45k • written 12.2 years ago by
lyz10302012
▴ 470
211
votes
21
replies
197k
views
12 follow
Forward And Reverse Strand Conventions
sequence
strand
updated 2.3 years ago by
Istvan Albert
102k • written 14.4 years ago by
Andrea_Bio
★ 2.9k
293
votes
40
replies
195k
views
30 follow
Tutorial:
How to download raw sequence data from GEO/SRA
fastq
SRA
bam
GEO
updated 4 months ago by
geocarvalho
▴ 390 • written 10.6 years ago by
Obi Griffith
20k
133
votes
19
replies
192k
views
13 follow
What'S The Difference Between Cds And Orf?
cds
orf
updated 3.9 years ago by
kajumi
• 0 • written 12.8 years ago by
shiy05
▴ 370
152
votes
42
replies
185k
views
22 follow
How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
heatmap
r
updated 2.8 years ago by
Ram
45k • written 13.0 years ago by
Obi Griffith
20k
124
votes
13
replies
183k
views
13 follow
How Can I Convert Bam To Sam?
bam
next-gen-sequencing
sam
updated 18 months ago by
Ram
45k • written 14.7 years ago by
Biomed
5.0k
99
votes
39
replies
180k
views
19 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 23 months ago by
Dan
▴ 180 • written 12.7 years ago by
abi
▴ 390
136
votes
18
replies
178k
views
16 follow
Blast - Formatting Output
blast
format
output
updated 2.3 years ago by
katieostrouchov
▴ 30 • written 11.3 years ago by
timjoncooper
▴ 320
143
votes
14
replies
172k
views
16 follow
What Is The Sequencing 'Depth' ?
next-gen
sequencing
updated 16 months ago by
Ram
45k • written 14.9 years ago by
Pierre Lindenbaum
165k
835
votes
169
replies
170k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 5 months ago by
Biostar
3.4k • written 8.3 years ago by
Istvan Albert
102k
75
votes
10
replies
162k
views
6 follow
Fold change - a final explanation
RNA-Seq
updated 4.5 years ago by
naloy
▴ 10 • written 6.4 years ago by
Sebastian Hesse
▴ 350
231
votes
38
replies
155k
views
29 follow
Tool:
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
ensembl
genome-coordinates
liftover
updated 21 months ago by
Ram
45k • written 12.0 years ago by
Malachi Griffith
20k
71
votes
18
replies
150k
views
14 follow
from .BAM to .BAI using samtools
next-gen-sequencing
samtools
updated 13 months ago by
Pierre Lindenbaum
165k • written 10.4 years ago by
Kizuna
▴ 880
367
votes
82
replies
150k
views
35 follow
Tool:
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel
next-gen
ngs
updated 11 months ago by
jena
▴ 320 • written 12.1 years ago by
ole.tange
★ 4.5k
0
votes
2
replies
147k
views
FastTree error: Non-unique name 'xxxxx' in the alignment
fasttree
orthofinder
phylogeny
mafft
6 months ago by
eedeaguiar
• 0
150
votes
33
replies
146k
views
27 follow
Useful Bash Commands To Handle Fasta Files
command-line
fasta
bash
updated 5 months ago by
Ram
45k • written 13.1 years ago by
Anima Mundi
★ 2.9k
169
votes
52
replies
140k
views
28 follow
Fastq Convert To Fasta
perl
11.4 years ago by
biolab
★ 1.4k
13
votes
8
replies
139k
views
7 follow
Convert A Text File Into A Fasta File
fasta
updated 2.4 years ago by
Ram
45k • written 13.4 years ago by
Zhshqzyc
▴ 520
78
votes
26
replies
136k
views
15 follow
How to count fastq reads
sequence
next-gen
fastq
reads
updated 15 months ago by
cschu181
★ 2.8k • written 9.9 years ago by
Chenglin
▴ 260
103
votes
9
replies
135k
views
11 follow
How To Merge Two Fastq.Gz Files?
merge
fastq
updated 2.9 years ago by
henry-keen
▴ 40 • written 11.5 years ago by
newDNASeqer
▴ 790
129
votes
33
replies
135k
views
31 follow
Is There A Free Alternative To Ingenuity Pathway Analysis?
network
pathway
updated 9 months ago by
lijoli
• 0 • written 14.0 years ago by
Gon
▴ 540
10
votes
4
replies
135k
views
How To Count The Number Of Elements In A Column Other Than 'X' In R
r
programming
updated 13.7 years ago by
Stefano Berri
4.4k • written 13.7 years ago by
Don
▴ 20
126
votes
7
replies
131k
views
Bam And Indexed Bam Files
bam
index
13.2 years ago by
Sahel
▴ 270
24
votes
9
replies
130k
views
8 follow
How to calculate "fold changes" in gene expression?
R
gene
updated 2.1 years ago by
Ram
45k • written 9.9 years ago by
juan.rosas1
▴ 70
119
votes
25
replies
126k
views
12 follow
Where Can I Download Human Reference Genome In Fasta Format? Hgref.Fa File
human
fasta
sequence
bwa
updated 8.1 years ago by
Hajk-Georg Drost
▴ 180 • written 14.7 years ago by
Biomed
5.0k
26
votes
10
replies
125k
views
Calculating P-Values From Z-Scores
statistics
r
updated 2.7 years ago by
Ram
45k • written 13.1 years ago by
Diana
▴ 930
103
votes
34
replies
124k
views
23 follow
How To Split A Bam File By Chromosome
bam
updated 14 months ago by
Ram
45k • written 12.8 years ago by
GPR
▴ 390
3
votes
3
replies
124k
views
Find mismatch in two columns in a data frame in R
R
updated 9.0 years ago by
dan.shea
▴ 10 • written 9.0 years ago by
dirranrak
▴ 20
309
votes
33
replies
123k
views
26 follow
Tutorial:
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 6 months ago by
tshtatland
▴ 190 • written 11.4 years ago by
Obi Griffith
20k
109
votes
15
replies
122k
views
16 follow
Convertion Of Gff3 To Gtf
gtf
gff
updated 12 months ago by
xiaoleiusc
▴ 140 • written 12.8 years ago by
GouthamAtla
12k
67
votes
9
replies
121k
views
10 follow
Blog:
Gene expression units explained: RPM, RPKM, FPKM and TPM
gene-expression
RNA-Seq
updated 2.1 years ago by
Ram
45k • written 7.5 years ago by
Renesh
★ 2.2k
57
votes
15
replies
117k
views
11 follow
Tutorial:
Using R in Conda
R
updated 7 months ago by
henry-keen
▴ 40 • written 4.7 years ago by
rohitsatyam102
▴ 930
46
votes
10
replies
117k
views
8 follow
Which Expression Units To Use, Fpkm Or Rpkm ?
fpkm
rpkm
rna-seq
updated 2.3 years ago by
Ram
45k • written 12.0 years ago by
biorepine
★ 1.5k
115
votes
21
replies
115k
views
14 follow
When To Choose Python Over Perl (And Vice Versa)?
python
perl
comparison
updated 13.0 years ago by
Aditya Joshi
▴ 30 • written 13.4 years ago by
Niek De Klein
★ 2.6k
126
votes
56
replies
113k
views
24 follow
How to plot coverage and depth statistics of a bam file
bam
coverage
depth
next-gen-sequencing
updated 17 months ago by
William
▴ 40 • written 10.7 years ago by
kay
▴ 380
95
votes
23
replies
112k
views
15 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools
samtools
htslib
updated 14 months ago by
clara.apicella
• 0 • written 6.6 years ago by
otwtgin2010
▴ 630
91
votes
10
replies
110k
views
11 follow
Best Way To Do Pathway Analysis Of A Set Of Genes?
protein
genes
pathway
analysis
function
updated 12.9 years ago by
Guangchuang Yu
★ 2.6k • written 12.9 years ago by
Wayne
★ 1.0k
118
votes
15
replies
108k
views
15 follow
Economics Of A Career In Bioinformatics
career
updated 14.2 years ago by
Mona Mohamed
• 0 • written 14.4 years ago by
Terence
▴ 210
86
votes
16
replies
108k
views
9 follow
Number of mapped reads from BAM file
bam
sam
reads
mapping
updated 2.3 years ago by
bhanu.chandra1
▴ 50 • written 9.9 years ago by
Prakki Rama
★ 2.7k
28
votes
8
replies
107k
views
7 follow
How To Calculate Fpkm (Fragments Per Kilobase Of Exon Per Million Fragments Mapped)
rna
fpkm
rpkm
written 14.0 years ago by
User 5402
▴ 210
241
votes
176
replies
105k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
Survival
TCGA
updated 22 months ago by
Ram
45k • written 9.6 years ago by
TriS
★ 4.7k
172
votes
41
replies
105k
views
27 follow
Multiline Fasta To Single Line Fasta
fasta
updated 18 months ago by
Ram
45k • written 13.8 years ago by
Palu
▴ 250
120,713 results • Page
1 of 2415
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Difference between gam and sam/bam files?
Comment: How to convert .ab1 to fastq
A: AB1 to FASTQ
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Recent Replies
Comment: How to convert .ab1 to fastq
by
Pierre Lindenbaum
165k
https://www.biostars.org/p/309727/
Answer: Parsing BAM file per cell from Smart-Seq2 dataset
by
dsull
★ 7.3k
Look at the STARsolo documentation on GitHub: it shows you how to create your manifest.tsv file so that the RG flag in your BAM file conta…
Answer: Gene Expression Timeline Analysis for N=1
by
ATpoint
87k
You say time series but it's actually discrete treatments, so no time series. It is an unreplicated within patient. I would probably apply …
Comment: Parsing BAM file per cell from Smart-Seq2 dataset
by
GenoMax
149k
Based on your use of UMI's you appear to have smartseq v.3 data. Since this is single cell data I don't know if plain `STAR` is appropria…
Answer: Interactive UMAP for scRNA-seq Data
by
S
• 0
Hi, I found a great package called [ShinyCell][1] which makes interactive UMAP and many other interactive plots. It's super easy to setu…
Comment: Where Is The Experimental Rna Structure Data?
by
Wayne
★ 2.1k
Related 2025 pre-print: ['NucleoSeeker: Precision Filtering of RNA Databases to Curate High-Quality Datasets'](https://www.biorxiv.org/cont…
Comment: GERP Score for variants
by
Begonia_pavonina
▴ 210
It seems that the link http://mendel.stanford.edu/SidowLab/downloads/gerp/ is dead now. Would anyone know if it is temporary of definitive?…
Comment: Help with CIBERSORTx Error in Single-Cell RNA-seq Analysis: Invalid 'times' Argu
by
jared.andrews07
★ 18k
Well, the issue is what it says. You're saying your reference data is single cell, but there's only a single cell for each cell type. It ex…
Answer: How to clarify results from an HLA association analysis - Omnibus tests/HATK/oth
by
grover.sandeep
▴ 20
https://pubmed.ncbi.nlm.nih.gov/37495751/ You can reach me. Sandeep Grover
Comment: enrichGo problem
by
Arup Ghosh
3.3k
Can you share some of the gene names from the `genes` vector?
Comment: nanopore variant calling
by
colindaven
7.3k
You'll get massive coverage for just one gene (maybe 2000+ depending on how long you run the minion for), so you could consider multiple ge…
Comment: Reasoning - Why is it invalid to compare ratios of TPMs?
by
ATpoint
87k
I can only speak for myself, but I have never looked at gene ratios, nor do I see its usecase.
Comment: Alignment algorithm for DNA sequencing
by
ATpoint
87k
> some alignment of DNA sequencing This is not an adequate description of what you achieve to do. Please say why common tools, such as the…
Comment: Alignment algorithm for DNA sequencing
by
GenoMax
149k
You can use `bbmap` with the `local=t` option if you need local alignments. `bowtie v.1.x` does ungapped alignments.
Answer: RepeatMasker UCSC track
by
Michael
55k
> These sequences are located in different regions of the genome and they have different lengths. Err, you are talking about repeats here,…
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