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110,427 results • Page
1 of 2209
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 12 weeks 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
43
votes
24
replies
196k
views
25 follow
How To Update R In Ubuntu ?
r
ubuntu
updated 14 months ago by
matthew.pace
▴ 50 • written 9.5 years ago by
Arpitha Hebbar
▴ 210
62
votes
14
replies
185k
views
9 follow
How To Deal With Duplicate Row Names Error In R
r
updated 5 weeks ago by
zx8754
11k • written 10.3 years ago by
Diana
▴ 900
12
votes
6
replies
183k
views
How can I uninstall my packages in Rstudio
R
Bioconductor
updated 2.7 years ago by
zx8754
11k • written 5.3 years ago by
hassanlou110
▴ 40
118
votes
31
replies
180k
views
17 follow
Correct Way To Parse A Fasta File In Python
fasta
parsing
python
updated 20 months ago by
GenoMax
129k • written 13.1 years ago by
Eric Normandeau
11k
151
votes
42
replies
176k
views
22 follow
How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
heatmap
r
updated 12 months ago by
Ram
39k • written 11.2 years ago by
Obi Griffith
20k
126
votes
19
replies
173k
views
13 follow
What'S The Difference Between Cds And Orf?
cds
orf
updated 2.1 years ago by
kajumi
• 0 • written 11.0 years ago by
shiy05
▴ 350
277
votes
39
replies
168k
views
29 follow
Tutorial:
How to download raw sequence data from GEO/SRA
fastq
SRA
bam
GEO
updated 9 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
142
votes
14
replies
165k
views
16 follow
What Is The Sequencing 'Depth' ?
next-gen
sequencing
updated 3.5 years ago by
Renesh
★ 2.1k • written 13.2 years ago by
Pierre Lindenbaum
154k
122
votes
11
replies
161k
views
11 follow
How Can I Convert Bam To Sam?
next-gen
sequencing
bam
sam
conversion
updated 21 months ago by
t.montserrat.ayuso
• 0 • written 12.9 years ago by
Biomed
4.9k
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
5 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
10
votes
4
replies
133k
views
How To Count The Number Of Elements In A Column Other Than 'X' In R
r
programming
updated 11.9 years ago by
Stefano Berri
4.4k • written 11.9 years ago by
Don
▴ 20
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
129
votes
32
replies
123k
views
29 follow
Is There A Free Alternative To Ingenuity Pathway Analysis?
network
pathway
updated 14 months ago by
Ram
39k • written 12.2 years ago by
Gon
▴ 530
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
160
votes
52
replies
119k
views
28 follow
Fastq Convert To Fasta
perl
9.6 years ago by
biolab
★ 1.4k
119
votes
25
replies
119k
views
12 follow
Where Can I Download Human Reference Genome In Fasta Format? Hgref.Fa File
human
fasta
sequence
bwa
updated 6.3 years ago by
Hajk-Georg Drost
▴ 160 • written 12.9 years ago by
Biomed
4.9k
98
votes
9
replies
115k
views
11 follow
How To Merge Two Fastq.Gz Files?
merge
fastq
updated 13 months ago by
henry-keen
▴ 40 • written 9.7 years ago by
newDNASeqer
▴ 750
3
votes
3
replies
114k
views
Find mismatch in two columns in a data frame in R
R
updated 7.2 years ago by
dan.shea
▴ 10 • written 7.2 years ago by
dirranrak
▴ 20
744
votes
162
replies
113k
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
115
votes
21
replies
111k
views
14 follow
When To Choose Python Over Perl (And Vice Versa)?
python
perl
comparison
updated 11.2 years ago by
Aditya Joshi
▴ 30 • written 11.6 years ago by
Niek De Klein
★ 2.6k
63
votes
16
replies
109k
views
11 follow
from .BAM to .BAI using samtools
sequencing
samtools
next-gen
updated 16 months ago by
Ram
39k • written 8.7 years ago by
Kizuna
▴ 860
118
votes
7
replies
108k
views
Bam And Indexed Bam Files
bam
index
11.4 years ago by
Sahel
▴ 260
91
votes
10
replies
106k
views
11 follow
Best Way To Do Pathway Analysis Of A Set Of Genes?
protein
genes
pathway
analysis
function
updated 11.2 years ago by
Guangchuang Yu
★ 2.6k • written 11.2 years ago by
Wayne
★ 1.0k
28
votes
8
replies
105k
views
7 follow
How To Calculate Fpkm (Fragments Per Kilobase Of Exon Per Million Fragments Mapped)
rna
fpkm
rpkm
written 12.2 years ago by
User 5402
▴ 210
118
votes
15
replies
102k
views
15 follow
Economics Of A Career In Bioinformatics
career
updated 12.4 years ago by
Mona Mohamed
• 0 • written 12.6 years ago by
Terence
▴ 210
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
98
votes
31
replies
100k
views
20 follow
How To Split A Bam File By Chromosome
bam
split
chromosome
updated 15 months ago by
Dan
▴ 120 • written 11.0 years ago by
GPR
▴ 390
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
31
votes
8
replies
96k
views
8 follow
How Do You Start Writing An Algorithm? Help Needed!
java
structure
algorithm
updated 12.4 years ago by
Hazel
• 0 • written 13.1 years ago by
Hazel
▴ 70
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 10 weeks ago by
Raag
• 0 • written 9.0 years ago by
kay
▴ 330
173
votes
30
replies
89k
views
17 follow
What Is The Best Method To Find Orthologous Genes Of A Species?
orthologues
updated 16 months ago by
Ram
39k • written 12.1 years ago by
Ct586
▴ 610
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
39
votes
8
replies
88k
views
samtools sorting and indexing
samtools
index
sort
updated 3.4 years ago by
onestop_data
▴ 320 • written 5.9 years ago by
ggman
▴ 80
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
70
votes
16
replies
86k
views
12 follow
What Does Samtools Flagstat Results Mean?
rna
samtools
mouse
updated 14 months ago by
Pierre Lindenbaum
154k • written 11.7 years ago by
Sakti
▴ 510
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
110,427 results • Page
1 of 2209
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Automated dbSNP lookup by rsID position, plus genome build liftover
Relatedness vs relatedness2 from vcftools give different results
A: Relatedness vs relatedness2 from vcftools give different results
Comment: LDheatmap will not accept LD matrix from Plink
LDheatmap will not accept LD matrix from Plink
A: mitochondrial/ribosomal protein genes in scRNA-seq analysis
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Comment: What does canonical transcript mean in the context of VEP
by
Pierre Lindenbaum
154k
https://www.ensembl.org/info/genome/genebuild/canonical.html > The Ensembl Canonical transcript is a single, representative transcript ide…
Answer: Why is coordinate sort required before findng read depths?
by
Ram
39k
In an unsorted BAM file, reads can be in any random order. In a co-ordinate sorted BAM file, reads are in the order in which they map to th…
Comment: What is "pident" (percentage of identical matches) in the "Diamond" protein alig
by
Alexander
▴ 70
how does it correspond to 27.2 ? or these are the other proteins ?
Comment: Merge different vcf files
by
Ram
39k
Normalize them first using `vt normalize` or `bcftools norm` - they need to be in left-aligned parsimonious representation before you can d…
Answer: integrate single cell RNA sequencing data
by
John Ma
▴ 300
You need to perform batch effect removal for these. Seurat has its integration protocol, and if you use scverse on Python, the usual choice…
Comment: What is "pident" (percentage of identical matches) in the "Diamond" protein alig
by
GenoMax
129k
I added the link for NCBI "book" since DIAMOND seems to follow the format/reporting structure for blast+ results. While the numbers shown i…
Comment: bcftools "--filter-logic" flag, what + means?
by
Ram
39k
`PASS` + `filter_name` is `filter_name`, not `PASS,filter_name`. PASS means the locus hit no filter. You'll never see a `PASS,<something>`.…
Comment: What is "pident" (percentage of identical matches) in the "Diamond" protein alig
by
Alexander
▴ 70
Thank you for the reply ! I got seems to be even more puzzled here - we see "identities" 95% while in the example "pident" is 27.2 - so …
Comment: bcftools "--filter-logic" flag, what + means?
by
Eugene A
▴ 170
Thanks a lot for the explanation!
Comment: How GATK pipeline called a homozygeous alternate allele (1/1) although one copy
by
Ram
39k
> Do you mean that because it is 1/1, so both copies is different from the reference and that is why the 0 in the AD is because no reads is…
Comment: What is "pident" (percentage of identical matches) in the "Diamond" protein alig
by
Alexander
▴ 70
Thank you ! @buchfink would you be so kind to comment ?
Comment: The famous WGS dataset, Ashkenazi Trio?
by
thadjudkins2
• 0
As the previous poster said we’re not sure what you’re looking for, but the basic data are available at the NCBI ftp site (linked from the …
Comment: Retrieving allele-specific information for a variant using VEP annotation
by
bt_cepo
▴ 20
Thank you both for your answers @masklin @ram ! For anyone facing the same problem, I followed Ram's suggestions and it worked beautifully…
Comment: how to Construct a Newick tree file from five large fasta files
by
gunala.nikhil
• 0
I need a phylogenetic tree for those 5 genomes
Comment: featurecounts not working on mirbase annotation file
by
GenoMax
129k
What does your `featureCounts` command line looks like?
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