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226
votes
39
replies
281k
views
33 follow
Gene Id Conversion Tool
mapping conversion
updated 7 months ago by 38k • written 13.4 years ago by ▴ 620
64
votes
3
replies
268k
views
Understanding up and down regulated genes from LOG2 foldchange or foldchange
protein gene-expression RNA-Seq
updated 19 days ago by 38k • written 8.8 years ago by ▴ 960
267
votes
29
replies
251k
views
25 follow
How To Filter Mapped Reads With Samtools
samtools
updated 4 months ago by 38k • written 10.4 years ago by ▴ 610
319
votes
90
replies
214k
views
57 follow
Tools To Calculate Average Coverage For A Bam File?
coverage bam sequencing
updated 6 months ago by 38k • written 12.2 years ago by 4.8k
43
votes
24
replies
193k
views
25 follow
How To Update R In Ubuntu ?
r ubuntu
updated 11 months ago by ▴ 50 • written 9.3 years ago by ▴ 210
59
votes
12
replies
182k
views
7 follow
How To Deal With Duplicate Row Names Error In R
r
updated 15 months ago by 38k • written 10.1 years ago by ▴ 900
12
votes
6
replies
179k
views
How can I uninstall my packages in Rstudio
R Bioconductor
updated 2.6 years ago by 11k • written 5.2 years ago by ▴ 40
118
votes
31
replies
174k
views
17 follow
Correct Way To Parse A Fasta File In Python
fasta parsing python
updated 18 months ago by 127k • written 13.0 years ago by 11k
151
votes
42
replies
174k
views
22 follow
How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
heatmap r
updated 10 months ago by 38k • written 11.1 years ago by 20k
124
votes
19
replies
171k
views
13 follow
What'S The Difference Between Cds And Orf?
cds orf
updated 23 months ago by • 0 • written 10.8 years ago by ▴ 350
276
votes
39
replies
164k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA bam GEO
updated 1 day ago by 38k • written 8.6 years ago by 20k
142
votes
14
replies
163k
views
16 follow
What Is The Sequencing 'Depth' ?
next-gen sequencing
updated 3.3 years ago by ★ 2.1k • written 13.0 years ago by 153k
188
votes
21
replies
163k
views
11 follow
Forward And Reverse Strand Conventions
sequence strand
updated 4 months ago by 97k • written 12.4 years ago by ★ 2.8k
122
votes
11
replies
158k
views
11 follow
How Can I Convert Bam To Sam?
next-gen sequencing bam sam conversion
updated 19 months ago by • 0 • written 12.7 years ago by 4.8k
133
votes
18
replies
154k
views
16 follow
Blast - Formatting Output
blast format output
updated 3 months ago by ▴ 20 • written 9.3 years ago by ▴ 310
158
votes
8
replies
151k
views
Generate vcf.gz file and its index file vcf.gz.tbi
vcf tabix
updated 8 months ago by 38k • written 10.3 years ago by ▴ 430
358
votes
79
replies
136k
views
34 follow
Tool: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel next-gen ngs
updated 4 months ago by 38k • written 10.1 years ago by ★ 4.3k
223
votes
38
replies
134k
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 3 months ago by ▴ 90 • written 10.1 years ago by 19k
10
votes
4
replies
132k
views
How To Count The Number Of Elements In A Column Other Than 'X' In R
r programming
updated 11.7 years ago by 4.3k • written 11.7 years ago by ▴ 20
90
votes
38
replies
128k
views
18 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 6 months ago by ▴ 10 • written 10.7 years ago by ▴ 370
143
votes
30
replies
126k
views
25 follow
Useful Bash Commands To Handle Fasta Files
command-line command-line fasta list bash
updated 6 months ago by 38k • written 11.1 years ago by ★ 2.9k
129
votes
32
replies
122k
views
29 follow
Is There A Free Alternative To Ingenuity Pathway Analysis?
network pathway
updated 11 months ago by 38k • written 12.1 years ago by ▴ 530
23
votes
9
replies
121k
views
8 follow
How to calculate "fold changes" in gene expression?
R gene
updated 6 weeks ago by 38k • written 7.9 years ago by ▴ 70
26
votes
10
replies
120k
views
Calculating P-Values From Z-Scores
statistics r
updated 9 months ago by 38k • written 11.1 years ago by ▴ 900
117
votes
25
replies
118k
views
12 follow
Where Can I Download Human Reference Genome In Fasta Format? Hgref.Fa File
human fasta sequence bwa
updated 6.1 years ago by ▴ 160 • written 12.7 years ago by 4.8k
13
votes
8
replies
118k
views
7 follow
Convert A Text File Into A Fasta File
fasta
updated 5 months ago by 38k • written 11.4 years ago by ▴ 500
160
votes
52
replies
116k
views
28 follow
Fastq Convert To Fasta
perl
9.4 years ago by biolab ★ 1.4k
97
votes
9
replies
113k
views
11 follow
How To Merge Two Fastq.Gz Files?
merge fastq
updated 11 months ago by ▴ 40 • written 9.5 years ago by ▴ 750
3
votes
3
replies
113k
views
Find mismatch in two columns in a data frame in R
R
updated 7.0 years ago by ▴ 10 • written 7.0 years ago by ▴ 20
46
votes
10
replies
112k
views
8 follow
Which Expression Units To Use, Fpkm Or Rpkm ?
fpkm rpkm rna-seq
updated 3 months ago by 38k • written 10.0 years ago by ★ 1.5k
115
votes
21
replies
111k
views
14 follow
When To Choose Python Over Perl (And Vice Versa)?
python perl comparison
updated 11.0 years ago by ▴ 30 • written 11.4 years ago by ★ 2.6k
730
votes
161
replies
108k
views
100 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 11 days ago by 1.6k • written 6.3 years ago by 97k
118
votes
7
replies
106k
views
Bam And Indexed Bam Files
bam index
11.2 years ago by Sahel ▴ 260
91
votes
10
replies
105k
views
11 follow
Best Way To Do Pathway Analysis Of A Set Of Genes?
protein genes pathway analysis function
updated 11.0 years ago by ★ 2.6k • written 11.0 years ago by ★ 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 12.0 years ago by ▴ 210
63
votes
16
replies
105k
views
11 follow
from .BAM to .BAI using samtools
sequencing samtools next-gen
updated 14 months ago by 38k • written 8.5 years ago by ▴ 860
118
votes
15
replies
101k
views
15 follow
Economics Of A Career In Bioinformatics
career
updated 12.2 years ago by • 0 • written 12.4 years ago by ▴ 210
73
votes
25
replies
97k
views
14 follow
How to count fastq reads
sequence next-gen fastq reads
updated 8 months ago by 38k • written 7.9 years ago by ▴ 250
100
votes
15
replies
97k
views
15 follow
Convertion Of Gff3 To Gtf
gtf gff
updated 21 days ago by ▴ 20 • written 10.8 years ago by 12k
96
votes
31
replies
96k
views
20 follow
How To Split A Bam File By Chromosome
bam split chromosome
updated 13 months ago by ▴ 90 • written 10.8 years ago by ▴ 390
31
votes
8
replies
96k
views
8 follow
How Do You Start Writing An Algorithm? Help Needed!
java structure algorithm
updated 12.2 years ago by • 0 • written 12.9 years ago by ▴ 70
59
votes
9
replies
94k
views
10 follow
Blog: Gene expression units explained: RPM, RPKM, FPKM and TPM
gene-expression RNA-Seq
updated 6 weeks ago by 38k • written 5.5 years ago by ★ 2.1k
274
votes
33
replies
92k
views
25 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 24 days ago by 38k • written 9.4 years ago by 20k
173
votes
30
replies
88k
views
17 follow
What Is The Best Method To Find Orthologous Genes Of A Species?
orthologues
updated 14 months ago by 38k • written 12.0 years ago by ▴ 610
118
votes
53
replies
88k
views
22 follow
How to plot coverage and depth statistics of a bam file
bam coverage depth next-gen-sequencing
updated 6 days ago by • 0 • written 8.8 years ago by ▴ 330
97
votes
19
replies
87k
views
12 follow
How To Get The Sequence Of A Genomic Region From Ucsc?
sequence ucsc fasta
updated 7 months ago by 38k • written 13.1 years ago by 27k
39
votes
8
replies
86k
views
samtools sorting and indexing
samtools index sort
updated 3.2 years ago by ▴ 320 • written 5.7 years ago by ▴ 80
70
votes
16
replies
85k
views
12 follow
What Does Samtools Flagstat Results Mean?
rna samtools mouse
updated 12 months ago by 153k • written 11.5 years ago by ▴ 510
43
votes
15
replies
85k
views
9 follow
How Do I Count The Number Values Less Than X In A Column Using R ?
rna edger r counts
updated 8.3 years ago by 11k • written 12.0 years ago by ▴ 910
167
votes
41
replies
85k
views
27 follow
Multiline Fasta To Single Line Fasta
sequence fasta
updated 7 weeks ago by • 0 • written 11.8 years ago by ▴ 240
1,000 results • Page 1 of 20
Recent Votes
NCBI's IgBLAST version 1.21.0 is now available
Read lengths greater than insert length
Answer: Read lengths greater than insert length
How to find promoter sequence of a gene?
Answer: How to find promoter sequence of a gene?
Comment: How to find promoter sequence of a gene?
Answer: Is it possible to do DGE analysis using log 2 normalized data with EdgeR ?
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Recent Replies
Comment: Is it possible to do DGE analysis using log 2 normalized data with EdgeR ? by seidel 11k
What technology is the GEO data set derived from? Signal intensity implies a fluorescence read out (i.e. microarray). If that's the case, y…
Comment: Log2 FC Threshold by seidel 11k
Given that 0.2 is a 1.15 fold change (2^0.2) you're right to be skeptical, but there's no clear answer as to the significance. Consider tha…
Comment: Read lengths greater than insert length by GenoMax 127k
As I said above the adapters are each ~60 bp long so they add ~120 bp (5' and 3' end adapters) to the length of the DNA fragment. What you …
Comment: Problem with fatsq-dump by GenoMax 127k
Looks like the developers have an answer for this error: https://github.com/ncbi/sra-tools/issues/139 At least the program seems to be ins…
Comment: Read lengths greater than insert length by shpak.max ▴ 30
I'm not claiming that all fragment lengths are exactly 50, the typical range for my data is 45-60. However, my read lengths are all 150, so…
Answer: Read lengths greater than insert length by GenoMax 127k
Illumina libraries are made by adding adapters to the ends of DNA fragment(s). Those adapters themselves are about 60 nucleotides long. Not…
Answer: How to get fraction of unspliced reads for specific gene from scRNAseq Cell Rang by Rob 5.9k
If you have the raw data, you can easily get this information using [alevin-fry](https://www.nature.com/articles/s41592-022-01408-3). It pr…
Answer: Matching gene-expression data with clinical data: best practices. by pilargmarch ▴ 60
I really like using [the R/Bioconductor package TCGAbiolinks][1], it gives you clinical and expression data by patient ID. [1]: http…
Comment: Problem with fatsq-dump by Utpal • 0
with the command which fastq-dump it returns: ~/.conda/envs/sratoolkit_env/bin/fastq-dump With fastq-dump I get the following error …
Comment: Calculation method of RMSMappingQuality by zhangfish ▴ 40
Maybe, I think the formal (1) is correct for most situations (for example the earlier version of GATK). However, there are some changes in …
Comment: error in downloading of some accesions with fastq-dump by Utpal • 0
Hi, could you please let me know how to upgrade sratoolkit in centos? Thanks and regards,
Answer: How to get fraction of unspliced reads for specific gene from scRNAseq Cell Rang by benformatics 3.5k
I don't think you can get that information specifically: https://kb.10xgenomics.com/hc/en-us/articles/360021902671-Can-we-detect-splice-va…
Comment: Remove part of headers in FASTA file by Pierre Lindenbaum 153k
Use `cut -d ' '`
Comment: Problem running interproscan-5.15-54.0 for protein sequences by Pratyay • 0
Hi, can you guide me how to compile the src folder? Many thanks!
Comment: Matching gene-expression data with clinical data: best practices. by krushnach80 ★ 1.1k
You can check [this][1] [1]: https://www.linkedomics.org/
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