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117,120 results • Page
1 of 2343
Sort: Views
Rank
Views
Votes
Replies
65
votes
3
replies
296k
views
Understanding up and down regulated genes from LOG2 foldchange or foldchange
protein
gene-expression
RNA-Seq
updated 14 months ago by
Ram
44k • written 10.0 years ago by
Whoknows
▴ 960
226
votes
39
replies
289k
views
33 follow
Gene Id Conversion Tool
david
updated 7 months ago by
Ram
44k • written 14.6 years ago by
Renee
▴ 620
280
votes
29
replies
286k
views
25 follow
How To Filter Mapped Reads With Samtools
samtools
updated 18 months ago by
Ram
44k • written 11.6 years ago by
sohadb1357
▴ 640
334
votes
92
replies
241k
views
58 follow
Tools To Calculate Average Coverage For A Bam File?
coverage
bam
sequencing
updated 9 months ago by
kalavattam
▴ 190 • written 13.3 years ago by
Biomed
5.0k
43
votes
24
replies
206k
views
25 follow
How To Update R In Ubuntu ?
r
ubuntu
updated 2.1 years ago by
matthew.pace
▴ 60 • written 10.5 years ago by
Arpitha Hebbar
▴ 210
12
votes
6
replies
202k
views
How can I uninstall my packages in Rstudio
R
Bioconductor
updated 3.7 years ago by
zx8754
11k • written 6.3 years ago by
hassanlou110
▴ 40
120
votes
31
replies
200k
views
17 follow
Correct Way To Parse A Fasta File In Python
python
fasta
updated 6 months ago by
Ram
44k • written 14.1 years ago by
Eric Normandeau
11k
62
votes
14
replies
196k
views
9 follow
How To Deal With Duplicate Row Names Error In R
r
updated 13 months ago by
zx8754
11k • written 11.3 years ago by
Diana
▴ 910
288
votes
39
replies
184k
views
29 follow
Tutorial:
How to download raw sequence data from GEO/SRA
fastq
SRA
bam
GEO
updated 14 months ago by
Ram
44k • written 9.7 years ago by
Obi Griffith
20k
131
votes
19
replies
183k
views
13 follow
What'S The Difference Between Cds And Orf?
cds
orf
updated 3.1 years ago by
kajumi
• 0 • written 12.0 years ago by
shiy05
▴ 370
165
votes
8
replies
182k
views
Generate vcf.gz file and its index file vcf.gz.tbi
vcf
tabix
updated 22 months ago by
Ram
44k • written 11.4 years ago by
lyz10302012
▴ 450
209
votes
21
replies
181k
views
12 follow
Forward And Reverse Strand Conventions
sequence
strand
updated 18 months ago by
Istvan Albert
100k • written 13.5 years ago by
Andrea_Bio
★ 2.8k
152
votes
42
replies
181k
views
22 follow
How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
heatmap
r
updated 2.0 years ago by
Ram
44k • written 12.2 years ago by
Obi Griffith
20k
124
votes
13
replies
175k
views
13 follow
How Can I Convert Bam To Sam?
bam
next-gen-sequencing
sam
updated 8 months ago by
Ram
44k • written 13.9 years ago by
Biomed
5.0k
135
votes
18
replies
171k
views
16 follow
Blast - Formatting Output
blast
format
output
updated 17 months ago by
katieostrouchov
▴ 30 • written 10.4 years ago by
timjoncooper
▴ 320
143
votes
14
replies
169k
views
16 follow
What Is The Sequencing 'Depth' ?
next-gen
sequencing
updated 6 months ago by
Ram
44k • written 14.1 years ago by
Pierre Lindenbaum
162k
98
votes
39
replies
159k
views
19 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 13 months ago by
Dan
▴ 180 • written 11.9 years ago by
abi
▴ 390
231
votes
38
replies
147k
views
29 follow
Tool:
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
ensembl
genome-coordinates
liftover
updated 11 months ago by
Ram
44k • written 11.2 years ago by
Malachi Griffith
20k
362
votes
82
replies
144k
views
35 follow
Tool:
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel
next-gen
ngs
updated 8 weeks ago by
jena
▴ 290 • written 11.3 years ago by
ole.tange
★ 4.4k
800
votes
167
replies
144k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 4 months ago by
Biostar
2.8k • written 7.5 years ago by
Istvan Albert
100k
147
votes
31
replies
138k
views
26 follow
Useful Bash Commands To Handle Fasta Files
command-line
fasta
bash
updated 10 months ago by
Ram
44k • written 12.3 years ago by
Anima Mundi
★ 2.9k
10
votes
4
replies
134k
views
How To Count The Number Of Elements In A Column Other Than 'X' In R
r
programming
updated 12.9 years ago by
Stefano Berri
4.4k • written 12.9 years ago by
Don
▴ 20
68
votes
18
replies
132k
views
14 follow
from .BAM to .BAI using samtools
next-gen-sequencing
samtools
updated 3 months ago by
Pierre Lindenbaum
162k • written 9.6 years ago by
Kizuna
▴ 870
13
votes
8
replies
131k
views
7 follow
Convert A Text File Into A Fasta File
fasta
updated 19 months ago by
Ram
44k • written 12.5 years ago by
Zhshqzyc
▴ 520
129
votes
32
replies
130k
views
29 follow
Is There A Free Alternative To Ingenuity Pathway Analysis?
network
pathway
updated 2.1 years ago by
Ram
44k • written 13.2 years ago by
Gon
▴ 540
166
votes
52
replies
129k
views
28 follow
Fastq Convert To Fasta
perl
10.5 years ago by
biolab
★ 1.4k
101
votes
9
replies
128k
views
11 follow
How To Merge Two Fastq.Gz Files?
merge
fastq
updated 2.1 years ago by
henry-keen
▴ 40 • written 10.7 years ago by
newDNASeqer
▴ 760
23
votes
9
replies
127k
views
8 follow
How to calculate "fold changes" in gene expression?
R
gene
updated 15 months ago by
Ram
44k • written 9.1 years ago by
juan.rosas1
▴ 70
26
votes
10
replies
123k
views
Calculating P-Values From Z-Scores
statistics
r
updated 23 months ago by
Ram
44k • written 12.3 years ago by
Diana
▴ 910
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 7.3 years ago by
Hajk-Georg Drost
▴ 160 • written 13.8 years ago by
Biomed
5.0k
77
votes
26
replies
121k
views
15 follow
How to count fastq reads
sequence
next-gen
fastq
reads
updated 6 months ago by
cschu181
★ 2.8k • written 9.1 years ago by
Chenglin
▴ 260
3
votes
3
replies
120k
views
Find mismatch in two columns in a data frame in R
R
updated 8.2 years ago by
dan.shea
▴ 10 • written 8.2 years ago by
dirranrak
▴ 20
121
votes
7
replies
119k
views
Bam And Indexed Bam Files
bam
index
12.4 years ago by
Sahel
▴ 260
46
votes
10
replies
115k
views
8 follow
Which Expression Units To Use, Fpkm Or Rpkm ?
fpkm
rpkm
rna-seq
updated 17 months ago by
Ram
44k • written 11.1 years ago by
biorepine
★ 1.5k
103
votes
34
replies
114k
views
23 follow
How To Split A Bam File By Chromosome
bam
updated 4 months ago by
Ram
44k • written 12.0 years ago by
GPR
▴ 390
115
votes
21
replies
113k
views
14 follow
When To Choose Python Over Perl (And Vice Versa)?
python
perl
comparison
updated 12.2 years ago by
Aditya Joshi
▴ 30 • written 12.6 years ago by
Niek De Klein
★ 2.6k
105
votes
15
replies
113k
views
16 follow
Convertion Of Gff3 To Gtf
gtf
gff
updated 9 weeks ago by
xiaoleiusc
▴ 140 • written 12.0 years ago by
GouthamAtla
12k
66
votes
9
replies
111k
views
10 follow
Blog:
Gene expression units explained: RPM, RPKM, FPKM and TPM
gene-expression
RNA-Seq
updated 15 months ago by
Ram
44k • written 6.7 years ago by
Renesh
★ 2.2k
67
votes
10
replies
110k
views
6 follow
Fold change - a final explanation
RNA-Seq
updated 3.7 years ago by
naloy
▴ 10 • written 5.6 years ago by
Sebastian Hesse
▴ 340
298
votes
33
replies
109k
views
25 follow
Tutorial:
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 15 months ago by
Ram
44k • written 10.6 years ago by
Obi Griffith
20k
91
votes
10
replies
108k
views
11 follow
Best Way To Do Pathway Analysis Of A Set Of Genes?
protein
genes
pathway
analysis
function
updated 12.1 years ago by
Guangchuang Yu
★ 2.6k • written 12.1 years ago by
Wayne
★ 1.0k
28
votes
8
replies
106k
views
7 follow
How To Calculate Fpkm (Fragments Per Kilobase Of Exon Per Million Fragments Mapped)
rna
fpkm
rpkm
written 13.2 years ago by
User 5402
▴ 210
118
votes
15
replies
105k
views
15 follow
Economics Of A Career In Bioinformatics
career
updated 13.4 years ago by
Mona Mohamed
• 0 • written 13.5 years ago by
Terence
▴ 210
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
171
votes
41
replies
98k
views
27 follow
Multiline Fasta To Single Line Fasta
fasta
updated 8 months ago by
Ram
44k • written 12.9 years ago by
Palu
▴ 250
85
votes
16
replies
98k
views
9 follow
Number of mapped reads from BAM file
bam
sam
reads
mapping
updated 18 months ago by
bhanu.chandra1
▴ 50 • written 9.1 years ago by
Prakki Rama
★ 2.7k
31
votes
8
replies
97k
views
8 follow
How Do You Start Writing An Algorithm? Help Needed!
java
structure
algorithm
updated 13.4 years ago by
Hazel
• 0 • written 14.0 years ago by
Hazel
▴ 70
43
votes
8
replies
97k
views
samtools sorting and indexing
samtools
index
sort
updated 4.3 years ago by
onestop_data
▴ 330 • written 6.9 years ago by
ggman
▴ 90
239
votes
176
replies
96k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
Survival
TCGA
updated 12 months ago by
Ram
44k • written 8.8 years ago by
TriS
★ 4.7k
105
votes
31
replies
95k
views
18 follow
Best Way To Merge A Many Thousand Small Bam Files Into One Big Bam File?
bam
picard
samtools
merge
updated 5 months ago by
mmfansler
▴ 450 • written 12.9 years ago by
2184687-1231-83-
★ 5.1k
117,120 results • Page
1 of 2343
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Gene Set Enrichment Analysis
Comment: Unexpected read length from NGS
Answer: Unexpected read length from NGS
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Comment: How to scrape BioMart data from https://sorfs.ugent.be/ website
by
Pierre Lindenbaum
162k
did you ask the authors to restore their server ?
Comment: Single cell analysis: Unable to subset cells in seurat object using desired nFea
by
sc_analysis
• 0
Yes. But after applying: merged_seurat_objects_filtered <- subset(x = merged_seurat_objects, subset = nFeature_RNA > 200 & nFeature_R…
Comment: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
by
fracarb8
★ 1.6k
This [paper][1] provides a comparison of the three methods in different settings. [1]: https://genomebiology.biomedcentral.com/articles…
Comment: Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files
by
Deepthi
• 0
pop up with sam error . Error reading _rstarts[] array: 21720, 23124
Comment: Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files
by
ATpoint
82k
See me edit I just made for the fastq check.
Comment: Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files
by
Deepthi
• 0
Thanks will check and update here.
Answer: Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files
by
ATpoint
82k
bowtie -x idx file.fastq | samtools view -o out.bam You might be messing up things with these positional arguments. Use this above. Us…
Comment: Annotating single cell data automatically
by
Francesco
▴ 10
- In order to run Azimuth: ``` AzimuthClusters <- RunAzimuth(seurat_obj, reference = "pbmcref") ``` - singleR ``` surveyRefere…
Comment: Single cell analysis: Unable to subset cells in seurat object using desired nFea
by
fracarb8
★ 1.6k
You are not subsetting based on `nFeature`. You are subsetting based on `nFeature` **AND** `nCount` **AND** `perc mt`.
Answer: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
by
txema.heredia
▴ 130
Update: I ran CellBender on these samples and compared its results with SoupX and DecontX. vs SoupX: ![cellbender vs SoupX][1] …
Comment: Unexpected read length from NGS
by
QX
• 0
thank you all!
Comment: How to calculate nucleotide diversity (mtDNA, PacBio_data), Suggest me some tool
by
hashim.rana11
▴ 20
Initially, I tried using Samtools and BCFtools, followed by running a script in Python (PyCharm) to measure nucleotide diversity![nucleoti…
Comment: Best Practice On Variant Discovery For Bacteria?
by
Ruqaiya
• 0
I used HaploTypecaller but my plasmid reads are not present in the output vcf file ... but it's there in my input file
Answer: How to calculate nucleotide diversity (mtDNA, PacBio_data), Suggest me some tool
by
Michael
54k
Variants should be called using a specialized mitochondrial variant caller, e.g.: [GATK Mutect2 CallMt][1] Then, pi, Tajima's D, and oth…
Comment: Splitting query fasta file for Diamond Blastp make the process faster?
by
kmat
• 0
I used `seqkit split` to divide the query FASTA file into 10 parts and then ran `diamond blastp` on each file using 44 threads. The process…
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