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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 15 days ago by 38k • written 8.8 years ago by ▴ 960
267
votes
29
replies
250k
views
25 follow
How To Filter Mapped Reads With Samtools
samtools
updated 3 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 5 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
178k
views
How can I uninstall my packages in Rstudio
R Bioconductor
updated 2.5 years ago by 11k • written 5.1 years ago by ▴ 40
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 11.0 years ago by 20k
118
votes
31
replies
174k
views
17 follow
Correct Way To Parse A Fasta File In Python
fasta parsing python
updated 17 months ago by 127k • written 12.9 years ago by 11k
124
votes
19
replies
171k
views
13 follow
What'S The Difference Between Cds And Orf?
cds orf
updated 22 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 download GEO bam
updated 10 months 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 96k • written 12.4 years ago by ★ 2.8k
122
votes
11
replies
157k
views
11 follow
How Can I Convert Bam To Sam?
next-gen sequencing bam sam conversion
updated 18 months ago by • 0 • written 12.7 years ago by 4.8k
131
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
150k
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 3 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
121k
views
29 follow
Is There A Free Alternative To Ingenuity Pathway Analysis?
network pathway
updated 11 months ago by 38k • written 12.0 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
117k
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 10 months ago by ▴ 40 • written 9.5 years ago by ▴ 750
3
votes
3
replies
112k
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
727
votes
161
replies
108k
views
100 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 7 days ago by 1.6k • written 6.3 years ago by 96k
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
104k
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 17 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 12 months ago by ▴ 70 • 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 5 weeks ago by 38k • written 5.5 years ago by ★ 2.1k
274
votes
33
replies
91k
views
25 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 21 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 11.9 years ago by ▴ 610
118
votes
53
replies
87k
views
22 follow
How to plot coverage and depth statistics of a bam file
bam coverage depth next-gen-sequencing
updated 3 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 11 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 11.9 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
108,939 results • Page 1 of 2179
Recent Votes
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Gene Set Enrichment Analysis
Can I sort my bam files with Picard MergeSamFiles?
Answer: Problem generating a .vcf after upgrade of samtools and bcftools
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Recent Replies
Answer: activity of unloaded/unassembled Tn5 by callumjcparr • 0
So I hope someone is still interested in this. We have taken to preparing recombinant Tn5 now as it's much cheaper than commercial supp…
Comment: RNA-SEQ by ali • 0
thanks for your helping
Comment: TSS of protein coding genes by ConvolutedGenome ▴ 10
I am quite confused with GENCODE GTF file, So, within the GENCODE GTF file, I noticed that each (protein-coding) gene has multiple "transc…
Comment: Recommendation for (Alternative) Splicing analysis packages for bulk RNA-seq da by iraun 5.8k
Hi! I personally use [SplAdder][1], in case you want to add it to your list :). [1]: https://github.com/ratschlab/spladder
Answer: Problem generating a .vcf after upgrade of samtools and bcftools by Andy • 0
Really the only needed, that help worked, thank's
Comment: Active enhancers for mm39 by seidel 11k
Just curious what you mean by "active" enhancers. Enhancers are active in a given context (e.g. cell type developmental state, etc.), and m…
Comment: Creating loop for read groups using Picard by ntsopoul ▴ 20
try absolute paths navigate to the directory with cd and use pwd to get the absolute directory.
Comment: how to create interacting Hi-C peaks by rheab1230 ▴ 140
Thank you. I will use this package since I am more familiar with R
Comment: how to create interacting Hi-C peaks by rheab1230 ▴ 140
thank you. i will go through it
Comment: Fastqc report analysis by npavliukovec • 0
Yeah, after trimming and fastqc I will have to generate MultiQC plots and after do mapping with reference genome. As I know, for eukaryotes…
Comment: My fastq files(paired end) have different read number by kimgeng • 0
Oh, I see, Thank you however, I want to make vcf files with gatk haplotypecaller and GenotypeGVCFs. But I got some problems I have about 2.…
Answer: My fastq files(paired end) have different read number by ntsopoul ▴ 20
Yes, this is normal because depending on how you generate the bam file, the non-aligning reads are saved in the .bam file along the properl…
Answer: Can I use abundance from Tximport to compare the expression level of transcript by ntsopoul ▴ 20
No, you should not do that since the count matrix is not normalized. Also, the statistics for getting a pValue requires consideration of al…
Comment: Easy way to split VCF file by chromosome by Joana • 0
You need to run bcftools index on your vcf file before running the suggested command.
Comment: Fastqc report analysis by ntsopoul ▴ 20
I think you are fine, no worries. Will you go ahead an align the fastq files to a genome? Do you know how?
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