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1,000 results • Page
1 of 20
Sort: Views
Rank
Views
Votes
Replies
226
votes
39
replies
286k
views
33 follow
Gene Id Conversion Tool
david
updated 5 weeks ago by
Ram
41k • written 14.1 years ago by
Renee
▴ 620
65
votes
3
replies
284k
views
Understanding up and down regulated genes from LOG2 foldchange or foldchange
protein
gene-expression
RNA-Seq
updated 8 months ago by
Ram
41k • written 9.5 years ago by
Whoknows
▴ 960
328
votes
92
replies
230k
views
58 follow
Tools To Calculate Average Coverage For A Bam File?
coverage
bam
sequencing
updated 3 months ago by
kalavattam
▴ 190 • written 12.8 years ago by
Biomed
4.9k
62
votes
14
replies
191k
views
9 follow
How To Deal With Duplicate Row Names Error In R
r
updated 7 months ago by
zx8754
11k • written 10.8 years ago by
Diana
▴ 900
118
votes
31
replies
190k
views
17 follow
Correct Way To Parse A Fasta File In Python
python
fasta
updated 14 days ago by
Ram
41k • written 13.6 years ago by
Eric Normandeau
11k
282
votes
39
replies
176k
views
29 follow
Tutorial:
How to download raw sequence data from GEO/SRA
fastq
SRA
bam
GEO
updated 8 months ago by
Ram
41k • written 9.3 years ago by
Obi Griffith
20k
124
votes
13
replies
168k
views
13 follow
How Can I Convert Bam To Sam?
bam
next-gen-sequencing
sam
updated 12 weeks ago by
Ram
41k • written 13.4 years ago by
Biomed
4.9k
142
votes
14
replies
167k
views
16 follow
What Is The Sequencing 'Depth' ?
next-gen
sequencing
updated 17 days ago by
Ram
41k • written 13.6 years ago by
Pierre Lindenbaum
158k
135
votes
18
replies
165k
views
16 follow
Blast - Formatting Output
blast
format
output
updated 11 months ago by
katieostrouchov
▴ 30 • written 10.0 years ago by
timjoncooper
▴ 320
95
votes
39
replies
146k
views
19 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 7 months ago by
Dan
▴ 160 • written 11.4 years ago by
abi
▴ 380
231
votes
38
replies
142k
views
29 follow
Tool:
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
ensembl
genome-coordinates
liftover
updated 5 months ago by
Ram
41k • written 10.7 years ago by
Malachi Griffith
19k
361
votes
81
replies
141k
views
34 follow
Tool:
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel
next-gen
ngs
7 months ago by
ole.tange
★ 4.4k
146
votes
31
replies
133k
views
26 follow
Useful Bash Commands To Handle Fasta Files
command-line
fasta
bash
updated 4 months ago by
Ram
41k • written 11.8 years ago by
Anima Mundi
★ 2.9k
772
votes
164
replies
128k
views
107 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 7 weeks ago by
Biostar
2.3k • written 7.0 years ago by
Istvan Albert
99k
23
votes
9
replies
125k
views
8 follow
How to calculate "fold changes" in gene expression?
R
gene
updated 9 months ago by
Ram
41k • written 8.6 years ago by
juan.rosas1
▴ 70
66
votes
18
replies
120k
views
14 follow
from .BAM to .BAI using samtools
next-gen-sequencing
samtools
updated 5 months ago by
Ram
41k • written 9.1 years ago by
Kizuna
▴ 860
46
votes
10
replies
114k
views
8 follow
Which Expression Units To Use, Fpkm Or Rpkm ?
fpkm
rpkm
rna-seq
updated 11 months ago by
Ram
41k • written 10.7 years ago by
biorepine
★ 1.5k
76
votes
26
replies
112k
views
15 follow
How to count fastq reads
sequence
next-gen
fastq
reads
updated 5 days ago by
cschu181
★ 2.8k • written 8.6 years ago by
Chenglin
▴ 260
101
votes
34
replies
107k
views
23 follow
How To Split A Bam File By Chromosome
bam
split
chromosome
updated 8 weeks ago by
Jorge Amigo
14k • written 11.5 years ago by
GPR
▴ 390
100
votes
15
replies
106k
views
15 follow
Convertion Of Gff3 To Gtf
gtf
gff
updated 8 months ago by
Genetics
▴ 20 • written 11.5 years ago by
GouthamAtla
12k
64
votes
9
replies
104k
views
10 follow
Blog:
Gene expression units explained: RPM, RPKM, FPKM and TPM
gene-expression
RNA-Seq
updated 9 months ago by
Ram
41k • written 6.2 years ago by
Renesh
★ 2.2k
288
votes
33
replies
102k
views
25 follow
Tutorial:
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 9 months ago by
Ram
41k • written 10.1 years ago by
Obi Griffith
20k
121
votes
56
replies
97k
views
24 follow
How to plot coverage and depth statistics of a bam file
bam
coverage
depth
next-gen-sequencing
updated 8 weeks ago by
William
▴ 20 • written 9.4 years ago by
kay
▴ 340
170
votes
41
replies
93k
views
27 follow
Multiline Fasta To Single Line Fasta
fasta
updated 9 weeks ago by
Ram
41k • written 12.5 years ago by
Palu
▴ 250
97
votes
19
replies
92k
views
12 follow
How To Get The Sequence Of A Genomic Region From Ucsc?
ucsc
fasta
sequence
updated 5 weeks ago by
Ram
41k • written 13.8 years ago by
Giovanni M Dall'Olio
28k
238
votes
176
replies
90k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
Survival
TCGA
updated 6 months ago by
Ram
41k • written 8.3 years ago by
TriS
★ 4.7k
72
votes
20
replies
85k
views
15 follow
How To Get Ensembl Id (Gene, Transcript, Protein) Mapping Information?
ensembl
identifiers
mapping
updated 10 months ago by
Ram
41k • written 13.1 years ago by
Unode
▴ 180
98
votes
27
replies
83k
views
21 follow
Extract Sub-Set Of Regions From Vcf File
vcf
tabix
genome
filter
updated 6 months ago by
NIRJHAR
• 0 • written 11.5 years ago by
Rubal7
▴ 830
88
votes
22
replies
83k
views
14 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools
samtools
htslib
updated 4 months ago by
sifa.khan
• 0 • written 5.3 years ago by
otwtgin2010
▴ 580
162
votes
64
replies
82k
views
39 follow
Selecting Random Pairs From Fastq?
random
fastq
illumina
sequence
updated 10 weeks ago by
rohitsatyam102
▴ 780 • written 12.7 years ago by
Ketil
4.1k
18
votes
14
replies
81k
views
10 follow
BLAST Database error: No alias or index file found for nucleotide database
blast
blastn
sift
makeblastdb
updated 7 weeks ago by
Ken
• 0 • written 9.1 years ago by
arronslacey
▴ 320
185
votes
43
replies
81k
views
29 follow
Drawing Chromosome Ideograms With Data
ideogram
visualization
chromosome
updated 20 days ago by
Ram
41k • written 13.7 years ago by
Yuri
★ 1.6k
51
votes
14
replies
79k
views
10 follow
Tutorial:
Using R in Conda
R
updated 8 months ago by
Ram
41k • written 3.4 years ago by
rohitsatyam102
▴ 780
29
votes
10
replies
73k
views
9 follow
Tutorial:
Installing an updated R version (>=4.0) using conda
software-error
R
updated 8 months ago by
Ram
41k • written 2.7 years ago by
Nitin Narwade
★ 1.5k
196
votes
44
replies
70k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
microarray-analysis
bioconductor
updated 10 months ago by
Ram
41k • written 11.2 years ago by
Obi Griffith
20k
33
votes
17
replies
70k
views
14 follow
How To Draw A Heat Map For Gene Expression Data?
microarray
heatmap
updated 10 months ago by
Ram
41k • written 12.5 years ago by
Fahmida
▴ 80
116
votes
25
replies
68k
views
14 follow
Is My Bam File Sorted ?
bam
next-gen
sequencing
sort
updated 9 months ago by
Miguel
▴ 20 • written 12.8 years ago by
Pierre Lindenbaum
158k
51
votes
15
replies
66k
views
12 follow
Sequence Number Count In Fastq.Gz File
counts
sequence
fastq
updated 9 months ago by
Ram
41k • written 12.4 years ago by
Bioscientist
★ 1.7k
361
votes
58
replies
66k
views
44 follow
Forum:
Recommend Your Favorite Bioinformatics Books
education
books
updated 5 weeks ago by
Ram
41k • written 13.7 years ago by
Istvan Albert
99k
92
votes
18
replies
65k
views
12 follow
Sequence length from Fasta
fasta
updated 11 months ago by
Ram
41k • written 9.1 years ago by
bongbang
▴ 80
62
votes
22
replies
61k
views
16 follow
How To Convert Gencode Gtf Into Bed Format ?
gtf
bed
updated 11 months ago by
leshaker
• 0 • written 11.1 years ago by
biorepine
★ 1.5k
328
votes
54
replies
61k
views
45 follow
What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
genome
visualization
updated 20 days ago by
Ram
41k • written 13.7 years ago by
brentp
24k
157
votes
24
replies
61k
views
19 follow
Recommended Tools For Alternative Splicing Detection From Rna-Seq Data
alternative-splicing
splicing
rna-seq
updated 5 months ago by
Ram
41k • written 10.7 years ago by
Nicolas Rosewick
10k
149
votes
35
replies
61k
views
33 follow
Tutorial:
Tools For Metagenomic Data Analysis
metagenomics
next-gen
updated 9 months ago by
Ram
41k • written 11.0 years ago by
vijay
★ 1.6k
102
votes
30
replies
61k
views
25 follow
Tools To Find Gene Ontology Term Enrichment
gene
enrichment
updated 4 weeks ago by
Ram
41k • written 13.7 years ago by
Biostar User
★ 1.0k
1
vote
6
replies
59k
views
Error in read.table(file = file, header = header, sep = sep, quote = quote, : duplicate 'row.names' are not allowed
R
updated 8 months ago by
Ram
41k • written 6.9 years ago by
IOM
• 0
134
votes
22
replies
59k
views
15 follow
How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental Biologist/non-bioinformatician
gene
LIMMA
edgeR
updated 5 months ago by
Kevin Blighe
86k • written 6.0 years ago by
Mike
★ 1.9k
17
votes
6
replies
59k
views
Turn Off Blast Search On Reverse Complement Strand In Blastn
blast
sequence
updated 5 weeks ago by
Ram
41k • written 13.8 years ago by
Zhaorong
★ 1.4k
93
votes
19
replies
58k
views
18 follow
What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
phylogenetics-tree
updated 5 months ago by
Ram
41k • written 13.2 years ago by
Niek De Klein
★ 2.6k
85
votes
2
replies
57k
views
6 follow
Tutorial:
How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 9 months ago by
Ram
41k • written 10.4 years ago by
Eric Normandeau
11k
1,000 results • Page
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Recent Votes
Answer: Mapping quality in `vg giraffe`
Comment: Identify clusters of populations based on gene expression
Answer: How can I map coordinates between two strains of yeast?
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The Biostar Herald for Monday, November 27, 2023
Comment: use bioservices.UniProt (python) to map uniprot accession to [multiple] ensembl
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Recent Replies
Comment: How to do simple pathway analysis?
by
he1k
• 0
Hi [AK][1], I downloaded the KO.keg file. I was wondering what tool(s) you used to generate the "KO.tsv" file as you showed here. Thanks. …
Comment: How can I map coordinates between two strains of yeast?
by
dthorbur
▴ 840
I think that is an alternative to a synteny analysis, but I only know liftover in terms of annotations. OP asks for "coordinates between th…
Comment: Bowtie mapping for single_end read
by
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78k
I am sceptical any tweaking of parameters will make a notable difference. Parameters in bowtie are very good at default, and given it's ChI…
Comment: How can I map coordinates between two strains of yeast?
by
cmdcolin
★ 3.4k
would something like liftover not be recommended? honest question
Comment: Best practices for differential expression analysis with low-yield Nanopore/ONT
by
dthorbur
▴ 840
That's good. But I still suspect this data might be really difficult to analyse. I have a handful of suggestions I would do to assess wheth…
Comment: Identify clusters of populations based on gene expression
by
dthorbur
▴ 840
One gene might not be enough data to "cluster" based on expression. Unless I'm missing something, that would just be breaking a single cont…
Comment: Best practices for differential expression analysis with low-yield Nanopore/ONT
by
tw_140
• 0
Yes, I performed ribosome depletion using an RNAse H based method.
Comment: Circular genome browser
by
cmdcolin
★ 3.4k
that's great to hear. one "proxy" for interactive is looking at the JS based tools, many are web based and interactive as a result. I have …
Comment: R ComplexHeatmap - Dividing Column Annotation into Distinct Y-Axis Scales
by
TC_Chang
▴ 10
Hi jv, Thank you for your reply. Basically, I'm trying to generate the figure shown below with two different y-axis scales. Any suggestio…
Comment: Best practices for differential expression analysis with low-yield Nanopore/ONT
by
dthorbur
▴ 840
I don't have a suggestion for low yield DE analyses, but I am curious about the samples. Did you conduct any ribo-depletion steps prior to …
Answer: How can I map coordinates between two strains of yeast?
by
dthorbur
▴ 840
It sounds like you are looking for synteny between the two genomes. I'm assuming they are assembled, but that may not be the case. If so, […
Comment: Identify clusters of populations based on gene expression
by
Nitin Narwade
★ 1.5k
Why don't you just plot it on your UMAP If it is specific to one cluster/sub-population you should get a relatively high expression in that…
Answer: The difference blastn output when using subject and db options
by
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136k
Default `task` option is `megablast` for `blastn` which looks for `highly similar sequences` compared to `blastn` which is looking for `som…
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu
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136k
https://www.biostars.org/u/14684/ may comment on this but it may be the order of operations that is causing this. After the `tpe` is applie…
Comment: Construction of single sequence assembly out of contigs
by
colindaven
5.7k
Inspector (only for long reads) and Merqury for short reads are also pretty good methods for doing a QC of your assembly.
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