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226
votes
39
replies
284k
views
33 follow
Gene Id Conversion Tool
mapping conversion
updated 13 months ago by 40k • written 13.9 years ago by ▴ 620
65
votes
3
replies
281k
views
Understanding up and down regulated genes from LOG2 foldchange or foldchange
protein gene-expression RNA-Seq
updated 6 months ago by 40k • written 9.3 years ago by ▴ 960
273
votes
29
replies
267k
views
25 follow
How To Filter Mapped Reads With Samtools
samtools
updated 10 months ago by 40k • written 10.9 years ago by ▴ 630
327
votes
92
replies
226k
views
58 follow
Tools To Calculate Average Coverage For A Bam File?
coverage bam sequencing
updated 7 weeks ago by ▴ 180 • written 12.7 years ago by 4.9k
43
votes
24
replies
200k
views
25 follow
How To Update R In Ubuntu ?
r ubuntu
updated 17 months ago by ▴ 60 • written 9.8 years ago by ▴ 210
62
votes
14
replies
189k
views
9 follow
How To Deal With Duplicate Row Names Error In R
r
updated 5 months ago by 11k • written 10.6 years ago by ▴ 900
12
votes
6
replies
187k
views
How can I uninstall my packages in Rstudio
R Bioconductor
updated 3.1 years ago by 11k • written 5.7 years ago by ▴ 40
118
votes
31
replies
186k
views
17 follow
Correct Way To Parse A Fasta File In Python
fasta parsing python
updated 24 months ago by 134k • written 13.5 years ago by 11k
151
votes
42
replies
177k
views
22 follow
How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
heatmap r
updated 16 months ago by 40k • written 11.6 years ago by 20k
128
votes
19
replies
176k
views
13 follow
What'S The Difference Between Cds And Orf?
cds orf
updated 2.4 years ago by • 0 • written 11.3 years ago by ▴ 350
282
votes
39
replies
174k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA bam GEO
updated 6 months ago by 40k • written 9.1 years ago by 20k
197
votes
21
replies
171k
views
12 follow
Forward And Reverse Strand Conventions
sequence strand
updated 10 months ago by 98k • written 12.9 years ago by ★ 2.8k
142
votes
14
replies
167k
views
16 follow
What Is The Sequencing 'Depth' ?
next-gen sequencing
updated 3.8 years ago by ★ 2.1k • written 13.5 years ago by 157k
124
votes
13
replies
165k
views
13 follow
How Can I Convert Bam To Sam?
bam next-gen-sequencing sam
updated 21 days ago by 40k • written 13.2 years ago by 4.9k
163
votes
8
replies
165k
views
Generate vcf.gz file and its index file vcf.gz.tbi
vcf tabix
updated 14 months ago by 40k • written 10.8 years ago by ▴ 450
135
votes
18
replies
162k
views
16 follow
Blast - Formatting Output
blast format output
updated 9 months ago by ▴ 20 • written 9.8 years ago by ▴ 320
93
votes
39
replies
142k
views
19 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 5 months ago by ▴ 140 • written 11.2 years ago by ▴ 380
229
votes
38
replies
140k
views
29 follow
Tool: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
ensembl genome-coordinates liftover
updated 3 months ago by 40k • written 10.6 years ago by 19k
360
votes
81
replies
140k
views
34 follow
Tool: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel next-gen ngs
5 months ago by ole.tange ★ 4.3k
10
votes
4
replies
133k
views
How To Count The Number Of Elements In A Column Other Than 'X' In R
r programming
updated 12.2 years ago by 4.4k • written 12.2 years ago by ▴ 20
146
votes
31
replies
131k
views
26 follow
Useful Bash Commands To Handle Fasta Files
command-line fasta bash
updated 8 weeks ago by 40k • written 11.6 years ago by ★ 2.9k
129
votes
32
replies
125k
views
29 follow
Is There A Free Alternative To Ingenuity Pathway Analysis?
network pathway
updated 17 months ago by 40k • written 12.6 years ago by ▴ 530
13
votes
8
replies
124k
views
7 follow
Convert A Text File Into A Fasta File
fasta
updated 11 months ago by 40k • written 11.9 years ago by ▴ 520
23
votes
9
replies
124k
views
8 follow
How to calculate "fold changes" in gene expression?
R gene
updated 7 months ago by 40k • written 8.4 years ago by ▴ 70
762
votes
162
replies
123k
views
105 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 6 weeks ago by 2.0k • written 6.8 years ago by 98k
161
votes
52
replies
122k
views
28 follow
Fastq Convert To Fasta
perl
9.9 years ago by biolab ★ 1.4k
26
votes
10
replies
121k
views
Calculating P-Values From Z-Scores
statistics r
updated 15 months ago by 40k • written 11.6 years ago by ▴ 900
119
votes
25
replies
121k
views
12 follow
Where Can I Download Human Reference Genome In Fasta Format? Hgref.Fa File
human fasta sequence bwa
updated 6.6 years ago by ▴ 160 • written 13.2 years ago by 4.9k
98
votes
9
replies
120k
views
11 follow
How To Merge Two Fastq.Gz Files?
merge fastq
updated 17 months ago by ▴ 40 • written 10.0 years ago by ▴ 750
66
votes
18
replies
116k
views
14 follow
from .BAM to .BAI using samtools
next-gen-sequencing samtools
updated 3 months ago by 40k • written 9.0 years ago by ▴ 860
3
votes
3
replies
116k
views
Find mismatch in two columns in a data frame in R
R
updated 7.6 years ago by ▴ 10 • written 7.6 years ago by ▴ 20
46
votes
10
replies
114k
views
8 follow
Which Expression Units To Use, Fpkm Or Rpkm ?
fpkm rpkm rna-seq
updated 9 months ago by 40k • written 10.5 years ago by ★ 1.5k
115
votes
21
replies
112k
views
14 follow
When To Choose Python Over Perl (And Vice Versa)?
python perl comparison
updated 11.5 years ago by ▴ 30 • written 11.9 years ago by ★ 2.6k
119
votes
7
replies
111k
views
Bam And Indexed Bam Files
bam index
11.7 years ago by Sahel ▴ 260
76
votes
25
replies
108k
views
14 follow
How to count fastq reads
sequence next-gen fastq reads
updated 15 months ago by 40k • written 8.4 years ago by ▴ 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 11.5 years ago by ★ 2.6k • written 11.5 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 12.5 years ago by ▴ 210
99
votes
32
replies
105k
views
21 follow
How To Split A Bam File By Chromosome
bam split chromosome
updated 7 weeks ago by • 0 • written 11.3 years ago by ▴ 390
100
votes
15
replies
104k
views
15 follow
Convertion Of Gff3 To Gtf
gtf gff
updated 6 months ago by ▴ 20 • written 11.3 years ago by 12k
118
votes
15
replies
103k
views
15 follow
Economics Of A Career In Bioinformatics
career
updated 12.7 years ago by • 0 • written 12.9 years ago by ▴ 210
64
votes
9
replies
102k
views
10 follow
Blog: Gene expression units explained: RPM, RPKM, FPKM and TPM
gene-expression RNA-Seq
updated 7 months ago by 40k • written 6.0 years ago by ★ 2.1k
288
votes
33
replies
99k
views
25 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 7 months ago by 40k • written 9.9 years ago by 20k
31
votes
8
replies
96k
views
8 follow
How Do You Start Writing An Algorithm? Help Needed!
java structure algorithm
updated 12.7 years ago by • 0 • written 13.4 years ago by ▴ 70
121
votes
54
replies
95k
views
23 follow
How to plot coverage and depth statistics of a bam file
bam coverage depth next-gen-sequencing
updated 5 weeks ago by ▴ 20 • written 9.3 years ago by ▴ 340
170
votes
41
replies
91k
views
27 follow
Multiline Fasta To Single Line Fasta
fasta
updated 4 days ago by 40k • written 12.3 years ago by ▴ 250
43
votes
8
replies
91k
views
samtools sorting and indexing
samtools index sort
updated 3.7 years ago by ▴ 330 • written 6.2 years ago by ▴ 80
97
votes
19
replies
91k
views
12 follow
How To Get The Sequence Of A Genomic Region From Ucsc?
sequence ucsc fasta
updated 13 months ago by 40k • written 13.6 years ago by 28k
173
votes
30
replies
90k
views
17 follow
What Is The Best Method To Find Orthologous Genes Of A Species?
orthologues
updated 20 months ago by 40k • written 12.5 years ago by ▴ 610
85
votes
16
replies
90k
views
9 follow
Number of mapped reads from BAM file
bam sam reads mapping
updated 10 months ago by ▴ 50 • written 8.5 years ago by ★ 2.7k
70
votes
16
replies
88k
views
12 follow
What Does Samtools Flagstat Results Mean?
rna samtools mouse
updated 18 months ago by 157k • written 12.0 years ago by ▴ 510
1,000 results • Page 1 of 20
Recent Votes
How to assign read groups to bam files?
C: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
C: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
Answer: Which function is best for pathway analysis?
Comment: Hisat2 index and alignment question
Answer: Low Alignment rate
Answer: Unable to build applet in DNAnexus, .jar file not found
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Popular Question to bharata1803 ▴ 550
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Recent Replies
Answer: Fetch Fastq files directly for SRA data by Rob 6.2k
What is the accession for the project? Many — though not all — of the projects present in the NCBI SRA are also hosted in the European Nuc…
Comment: Dataset's name in BioMart for S. pombe by YUYANG.OON • 0
Works with `useMart(biomart="fungi_mart", dataset="spombe_eg_gene", host="https://fungi.ensembl.org")`
Comment: Bug of vg surject by Jordan M Eizenga ▴ 360
This is still hard to interpret without the commands. What would help is if you literally copied the full UNIX commands along with their re…
Comment: Which function is best for pathway analysis? by Chris ▴ 180
Thank you for your reply! Do you have code that I and others can implement? I am not sure how to customize the gmt file from my differentia…
Comment: Bug of vg surject by Qi • 0
Thanks your reply! my resulte show below: 5x_pan_sv.bam 1347587601 #converted from gam to bam F1 indel=0.830392 snp=0.932511 5…
Comment: Bug of vg surject by Jordan M Eizenga ▴ 360
It might help us to diagnose the problem if you included the exact commands that you used and showed the results that you are concerned abo…
Answer: Which function is best for pathway analysis? by Yogi ▴ 20
Few things to mention. Pathway Enrichment Analysis can be split into two categories. 1. Functional Class Scoring Methods 2. Overrepr…
Answer: identify DEGs across all conditions and per specific conditions by Yogi ▴ 20
Couple of things. (Feel free to correct if I'm misunderstanding). "DESeq2" is meant for 1v1 comparisons. If you're trying to compar…
Comment: Hisat2 index and alignment question by Istvan Albert 98k
yes correct you have to pass the full prefix and not the directory
Comment: Low Alignment rate by dsull ★ 4.7k
Wow! Didn't realize the repeat-masked file could have such a large influence on alignment. Very good to know -- I guess I'll need to dive i…
Comment: Troubles launch IGV on Linux(Debian) by morovatunc ▴ 550
Disclaimer: My comment could be totally unrelated. I would give these a try if you have noone comment/answer your problem. I have had this…
Comment: How to check RNAseq support for annotated genes? by Michael 53k
> I tried it using STAR to map the transcript to the annotation gtf file That is not what STAR is for. STAR is for aligning short reads in…
Comment: Low Alignment rate by Mehwish • 0
Thanks alot! This worked out for me https://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz …
Comment: Violin plot (Monocle 3) - Troubleshooting by Ram 40k
The error message tells me there is the possibility of a conflicting function called `plot_genes_violin` that accepts one parameter and err…
Comment: Violin plot (Monocle 3) - Troubleshooting by bk11 ★ 1.2k
I m not sure why you have problem there. I do not encounter any problem. May be your gene list are not present in your source object. Pleas…
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