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Limit : this year
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1,000 results • Page
1 of 20
Sort: Views
Rank
Views
Votes
Replies
226
votes
39
replies
282k
views
33 follow
Gene Id Conversion Tool
mapping
conversion
updated 9 months ago by
Ram
39k • written 13.6 years ago by
Renee
▴ 620
65
votes
3
replies
274k
views
Understanding up and down regulated genes from LOG2 foldchange or foldchange
protein
gene-expression
RNA-Seq
updated 3 months ago by
Ram
39k • written 9.0 years ago by
Whoknows
▴ 960
267
votes
29
replies
257k
views
25 follow
How To Filter Mapped Reads With Samtools
samtools
updated 6 months ago by
Ram
39k • written 10.6 years ago by
sohadb1357
▴ 610
323
votes
90
replies
219k
views
57 follow
Tools To Calculate Average Coverage For A Bam File?
coverage
bam
sequencing
updated 8 months ago by
Ram
39k • written 12.4 years ago by
Biomed
4.9k
62
votes
14
replies
186k
views
9 follow
How To Deal With Duplicate Row Names Error In R
r
updated 6 weeks ago by
zx8754
11k • written 10.3 years ago by
Diana
▴ 900
277
votes
39
replies
168k
views
29 follow
Tutorial:
How to download raw sequence data from GEO/SRA
fastq
SRA
bam
GEO
updated 10 weeks ago by
Ram
39k • written 8.8 years ago by
Obi Griffith
20k
193
votes
21
replies
166k
views
12 follow
Forward And Reverse Strand Conventions
sequence
strand
updated 6 months ago by
Istvan Albert
98k • written 12.6 years ago by
Andrea_Bio
★ 2.8k
135
votes
18
replies
158k
views
16 follow
Blast - Formatting Output
blast
format
output
updated 5 months ago by
katieostrouchov
▴ 20 • written 9.5 years ago by
timjoncooper
▴ 320
161
votes
8
replies
157k
views
Generate vcf.gz file and its index file vcf.gz.tbi
vcf
tabix
updated 10 months ago by
Ram
39k • written 10.5 years ago by
lyz10302012
▴ 430
360
votes
81
replies
138k
views
34 follow
Tool:
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel
next-gen
ngs
6 weeks ago by
ole.tange
★ 4.3k
224
votes
38
replies
136k
views
29 follow
Tool:
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
genome
coordinates
conversion
liftover
ensembl
Tool
updated 5 months ago by
harelarik
▴ 90 • written 10.3 years ago by
Malachi Griffith
19k
91
votes
39
replies
134k
views
19 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 6 weeks ago by
Dan
▴ 120 • written 10.9 years ago by
abi
▴ 370
143
votes
30
replies
128k
views
25 follow
Useful Bash Commands To Handle Fasta Files
command-line
command-line
fasta
list
bash
updated 8 months ago by
Ram
39k • written 11.3 years ago by
Anima Mundi
★ 2.9k
23
votes
9
replies
122k
views
8 follow
How to calculate "fold changes" in gene expression?
R
gene
updated 3 months ago by
Ram
39k • written 8.1 years ago by
juan.rosas1
▴ 70
26
votes
10
replies
121k
views
Calculating P-Values From Z-Scores
statistics
r
updated 11 months ago by
Ram
39k • written 11.3 years ago by
Diana
▴ 900
13
votes
8
replies
121k
views
7 follow
Convert A Text File Into A Fasta File
fasta
updated 8 months ago by
Ram
39k • written 11.6 years ago by
Zhshqzyc
▴ 520
744
votes
162
replies
114k
views
101 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 5 weeks ago by
Biostar
1.8k • written 6.5 years ago by
Istvan Albert
98k
46
votes
10
replies
112k
views
8 follow
Which Expression Units To Use, Fpkm Or Rpkm ?
fpkm
rpkm
rna-seq
updated 5 months ago by
Ram
39k • written 10.2 years ago by
biorepine
★ 1.5k
73
votes
25
replies
102k
views
14 follow
How to count fastq reads
sequence
next-gen
fastq
reads
updated 11 months ago by
Ram
39k • written 8.1 years ago by
Chenglin
▴ 250
100
votes
15
replies
100k
views
15 follow
Convertion Of Gff3 To Gtf
gtf
gff
updated 3 months ago by
Genetics
▴ 20 • written 11.0 years ago by
GouthamAtla
12k
63
votes
9
replies
97k
views
10 follow
Blog:
Gene expression units explained: RPM, RPKM, FPKM and TPM
gene-expression
RNA-Seq
updated 3 months ago by
Ram
39k • written 5.7 years ago by
Renesh
★ 2.1k
277
votes
33
replies
94k
views
25 follow
Tutorial:
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 3 months ago by
Ram
39k • written 9.6 years ago by
Obi Griffith
20k
120
votes
53
replies
90k
views
22 follow
How to plot coverage and depth statistics of a bam file
bam
coverage
depth
next-gen-sequencing
updated 11 weeks ago by
Raag
• 0 • written 9.0 years ago by
kay
▴ 330
97
votes
19
replies
89k
views
12 follow
How To Get The Sequence Of A Genomic Region From Ucsc?
sequence
ucsc
fasta
updated 9 months ago by
Ram
39k • written 13.3 years ago by
Giovanni M Dall'Olio
27k
167
votes
41
replies
88k
views
27 follow
Multiline Fasta To Single Line Fasta
sequence
fasta
updated 4 months ago by
Onur
• 0 • written 12.0 years ago by
Palu
▴ 240
84
votes
16
replies
86k
views
9 follow
Number of mapped reads from BAM file
bam
sam
reads
mapping
updated 6 months ago by
bhanu.chandra1
▴ 50 • written 8.1 years ago by
Prakki Rama
★ 2.6k
238
votes
176
replies
85k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
Survival
TCGA
updated 11 days ago by
Ram
39k • written 7.8 years ago by
TriS
★ 4.6k
101
votes
31
replies
84k
views
18 follow
Best Way To Merge A Many Thousand Small Bam Files Into One Big Bam File?
bam
picard
samtools
merge
updated 10 months ago by
Ram
39k • written 11.9 years ago by
2184687-1231-83-
★ 5.0k
79
votes
22
replies
83k
views
16 follow
How To Split One Big Sequence File Into Multiple Files With Less Than 1000 Sequences In A Single File
next-gen
sequencing
fasta
rna
r
perl
updated 6 months ago by
Ram
39k • written 11.6 years ago by
Hamilton
▴ 290
106
votes
45
replies
81k
views
30 follow
How To Extract A Sequence From A Big (6Gb) Multifasta File ?
fasta
updated 9 months ago by
aswinssoman
▴ 30 • written 10.9 years ago by
Mchimich
▴ 320
70
votes
20
replies
81k
views
15 follow
How To Get Ensembl Id (Gene, Transcript, Protein) Mapping Information?
ensembl
identifiers
mapping
updated 4 months ago by
Ram
39k • written 12.6 years ago by
Unode
▴ 180
185
votes
43
replies
79k
views
29 follow
Drawing Chromosome Ideograms With Data
chromosome
visualization
ideogram
updated 9 months ago by
Ram
39k • written 13.2 years ago by
Yuri
★ 1.6k
95
votes
27
replies
77k
views
21 follow
Extract Sub-Set Of Regions From Vcf File
vcf
tabix
genome
filter
updated 16 days ago by
NIRJHAR
• 0 • written 11.0 years ago by
Rubal7
▴ 820
160
votes
63
replies
76k
views
38 follow
Selecting Random Pairs From Fastq?
random
fastq
illumina
sequence
updated 4 days ago by
Ram
39k • written 12.2 years ago by
Ketil
4.1k
17
votes
12
replies
75k
views
8 follow
BLAST Database error: No alias or index file found for nucleotide database
blast
blastn
sift
makeblastdb
updated 9 months ago by
Luke
• 0 • written 8.6 years ago by
arronslacey
▴ 320
82
votes
21
replies
74k
views
13 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools
samtools
htslib
updated 3 months ago by
cmdcolin
★ 3.0k • written 4.9 years ago by
otwtgin2010
▴ 540
104
votes
12
replies
73k
views
7 follow
Bedtools Compare Multiple Bed Files?
bedtools
intersect
updated 7 months ago by
Ram
39k • written 11.6 years ago by
Bioscientist
★ 1.7k
67
votes
18
replies
70k
views
17 follow
Project For A Beginner Bioinformatics Student
project
java
updated 10 months ago by
Ram
39k • written 11.6 years ago by
And
▴ 230
33
votes
17
replies
69k
views
14 follow
How To Draw A Heat Map For Gene Expression Data?
microarray
heatmap
updated 4 months ago by
Ram
39k • written 12.0 years ago by
Fahmida
▴ 80
196
votes
44
replies
69k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
microarray-analysis
bioconductor
updated 4 months ago by
Ram
39k • written 10.7 years ago by
Obi Griffith
20k
188
votes
50
replies
68k
views
41 follow
How To Remove The Same Sequences In The Fasta Files?
fasta
sequence
duplicates
updated 8 months ago by
Ram
39k • written 12.6 years ago by
Zhangleisdau
▴ 340
40
votes
15
replies
66k
views
14 follow
Converting Affymetrix Probes To Gene Ids
affymetrix
conversion
entrez
updated 8 months ago by
Ram
39k • written 9.9 years ago by
Josh
▴ 140
74
votes
13
replies
66k
views
10 follow
Tutorial:
Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r
cancer
classification
updated 7 months ago by
Ram
39k • written 9.5 years ago by
Nicholas Spies
★ 1.2k
45
votes
14
replies
65k
views
10 follow
Tutorial:
Using R in Conda
R
updated 11 weeks ago by
Ram
39k • written 2.9 years ago by
rohitsatyam102
▴ 690
114
votes
25
replies
65k
views
14 follow
Is My Bam File Sorted ?
bam
next-gen
sequencing
sort
updated 3 months ago by
Miguel
▴ 10 • written 12.3 years ago by
Pierre Lindenbaum
154k
50
votes
15
replies
63k
views
12 follow
Sequence Number Count In Fastq.Gz File
counts
sequence
fastq
updated 3 months ago by
Ram
39k • written 11.9 years ago by
Bioscientist
★ 1.7k
54
votes
4
replies
63k
views
What is difference between soft-clipped and hard-clipped in SAM specification?
sequence
next-gen-sequencing
updated 7 months ago by
Ram
39k • written 8.6 years ago by
mangfu100
▴ 800
26
votes
10
replies
63k
views
9 follow
Tutorial:
Installing an updated R version (>=4.0) using conda
software-error
R
updated 12 weeks ago by
Ram
39k • written 2.2 years ago by
Nitin Narwade
★ 1.3k
40
votes
7
replies
63k
views
Clustering Data (Rna-Seq) Using R To Produce A Heatmap
r
rna
heatmap
clustering
gene
updated 11 months ago by
Ram
39k • written 11.6 years ago by
Kanne
▴ 450
361
votes
57
replies
61k
views
43 follow
Forum:
Recommend Your Favorite Bioinformatics Books
books
education
updated 8 months ago by
Kevin Blighe
85k • written 13.3 years ago by
Istvan Albert
98k
1,000 results • Page
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Recent Votes
Answer: calculate p value and associated z score for snp-gene pair
Answer: calculate p value and associated z score for snp-gene pair
Answer: I need help with a blast command, please help
Answer: I need help with a blast command, please help
Answer: NCBI API, Perl
Get a list of genes associated with a drug in 1 min
Answer: Getting species names and taxa id from assembly accession number
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Recent Replies
Comment: calculate p value and associated z score for snp-gene pair
by
rheab1230
▴ 140
Thank you so much for this. Yes, in this case I get all the SNPs. I also have one more question: SNP gene beta t-stat p-value FDR …
Comment: Is RNA-Seq well suited for studying pseudogenes and lncRNA?
by
rpolicastro
12k
lncRNAs are usually fine to include in downstream analysis since they are generally not selected against in most RNA-seq library prep proto…
Comment: I need help with a blast command, please help
by
neto.pvp
• 0
Thank you very much!! I'm new to this subject and I believe your answer gave me a great idea of where to go next, thanks again!!
Answer: NCBI API, Perl
by
GenoMax
129k
You are likely best served by using `NCBI datasets` ([**LINK**][1]) or `EntrezDirect` ([**LINK**][2]) command line tools. If you want to …
Comment: Obtain a --gene-trans-map file after rnaSPAdes
by
GenoMax
129k
You could try to create one: https://groups.google.com/g/trinityrnaseq-users/c/qPbWnLl4iY0 While this is from an unrelated software the so…
Comment: CNNScoreVariants Error
by
Pierre Lindenbaum
154k
that is another question
Comment: Difference between USCS exon coordinates and ensembl
by
amy__
▴ 50
Hi @atpoint, I went to http://genome.ucsc.edu/cgi-bin/hgTables and did: 1. ![enter image description here][1] then: 2. ![enter image…
Comment: should non-protein-coding rna(e.g. lncRNA) be removed in RNA-Seq differential ex
by
Kermit
▴ 80
See also: https://www.biostars.org/p/9535550/#9536086
Answer: Getting species names and taxa id from assembly accession number
by
MirianT_NCBI
▴ 590
Hi, As an alternative, you could use [NCBI Datasets][1] for this task. NCBI Datasets allows users to retrieve metadata reports in JSON or…
Comment: Optimum setting for local blastp for ~10K sequences
by
sodiumnitrate
▴ 20
Thank you for the info! It turned out that running all 10k at once is actually faster than running one or two at a time!
Answer: Installation of PPFinder
by
GenoMax
129k
Since the software is still [**listed on the Brent lab**][1] website your best bet would be to email the investigator and ask that they fix…
Comment: How to calculate TPM from featureCounts output
by
rpolicastro
12k
If you want to go that route, yes.
Comment: Difference between USCS exon coordinates and ensembl
by
ATpoint
72k
What did you download from UCSC? 1-off usually means one file is zero-based and the other 1-based. BED files from UCSC are 0-based, Ensembl…
Comment: Alignment of case vs. control from different origin
by
sativus
• 0
Thank you kindly for the explanation, it is highly appreciated. I suppose i was a bit confused as you quite often see people validating the…
Answer: Gene enrichment analysis
by
nux
▴ 10
Hello. For this you have to select 'hyper' as your method and then provide a complete list of genes which both include the candidate and no…
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