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49 results • Page
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Filtering for tag:
genome browser
•
reset
0
votes
2
replies
133
views
Discrepancy between Genome Browser hg19 phyloP Score and that of wig data
phyloP
genome browser
20 days ago by
progistar
• 0
0
votes
1
reply
166
views
Deletions together with SNVs on BAM files
alignment
sequencing
genome browser
21 days ago by
baliczap
• 0
0
votes
2
replies
106
views
getting fastq ID with SNPs
SNP
genome browser
fastq
5 weeks ago by
bitpir
▴ 190
2
votes
0
replies
111
views
News:
Free Ensembl Browser and REST API virtual workshops in March
Ensembl
training
REST API
workshop
genome browser
News
updated 5 weeks ago by
GenoMax
99k • written 5 weeks ago by
Michal @Ensembl
▴ 90
10
votes
11
replies
629
views
8 follow
Forum:
Best open source genome browser in 2020
genome browser
bioinformatics
genomics
Forum
updated 17 days ago by
lieven.sterck
10k • written 4 months ago by
mrmrwinter
▴ 30
1
vote
3
replies
1.7k
views
IGV or IGB
RNA-Seq
IGV
IGB
genome browser
NGS
updated 9 months ago by
xunshengbu
• 0 • written 2.3 years ago by
akivab2
▴ 110
5
votes
5
replies
275
views
Automate finding locations of BLASTN hits in genome browser?
BLASTN
Genome Browser
updated 12 months ago by
Alex Reynolds
32k • written 12 months ago by
jamie.pike
▴ 60
0
votes
4
replies
284
views
Error from Epigenome browser: "Tracks need to be hosted on a web server that is accessible by this browser server."
genome browser
epigenome browser
custom tracks
12 months ago by
zaranyjess
• 0
4
votes
6
replies
293
views
UCSC browser track description can't be updated
Browser
ucsc
genome browser
custom track
updated 14 months ago by
Luis Nassar
▴ 420 • written 14 months ago by
Sperber
▴ 10
8
votes
2
replies
439
views
Blog:
Which genome browser to use for my data?
IGV
Jbrowse
Genome browser
Visualization
Blog
updated 14 months ago by
cpad0112
15k • written 15 months ago by
Juke34
★ 5.3k
2
votes
3
replies
331
views
Getting CDS from chromosome positions
sequence
cds
genome browser
chromosome position
updated 16 months ago by
Luis Nassar
▴ 420 • written 17 months ago by
drmouradap
• 0
2
votes
1
reply
644
views
Locating telomere on a given chromosome
chromosome
telomere
centromere
genome browser
updated 16 months ago by
Luis Nassar
▴ 420 • written 20 months ago by
skiesareforflying
▴ 20
3
votes
3
replies
305
views
UCSC Genome Browser GENCODE Subtrack Label Highlighted?
ucsc
genome browser
visualization
updated 16 months ago by
Luis Nassar
▴ 420 • written 16 months ago by
skiesareforflying
▴ 20
1
vote
10
replies
2.3k
views
Maker Gff3 file issues
genome browser
genome annotation
JBrowse
updated 17 months ago by
zsdxgl
• 0 • written 2.4 years ago by
alslonik
▴ 180
2
votes
1
reply
312
views
understanding the data from the ucsc table browser
gene
genome
genome browser
introns
R
20 months ago by
a4appy23
▴ 10
55
votes
23
replies
2.7k
views
10 follow
Tool:
ASCIIGenome: Text Only Genome Viewer!
genome browser
terminal
java
ASCIIGenome
Tool
updated 2.5 years ago by
quokka
▴ 10 • written 4.7 years ago by
dariober
12k
2
votes
4
replies
1.7k
views
doubts about genome assembly and ensembl
Assembly
SNP
Ensembl
UCSC
Genome Browser
updated 2.5 years ago by
Biostar
20 • written 6.3 years ago by
palliyath91
• 0
2
votes
4
replies
1.6k
views
Extracting promoter sequence for reverse/minus strand gene from genome browser
Genome browser
Reverse strand gene
Promoter
updated 2.7 years ago by
Alex Reynolds
32k • written 2.8 years ago by
amy.bashir
▴ 80
0
votes
10
replies
870
views
Problems uploading custom track to UCSC Genome Browser
genome browser
UCSC
2.7 years ago by
rs
▴ 40
1
vote
1
reply
639
views
Do we discard variants with repetitive regions and do these masks mean repetition?
VCF
Genome Browser
3.1 years ago by
Dayna
▴ 20
5
votes
14
replies
1.4k
views
Files to compare ChIP vs Input on genome browser: after alignment or peak calling?
ChIP-seq
genome browser
MACS2
updated 3.1 years ago by
Friederike
6.9k • written 3.1 years ago by
salamandra
▴ 360
5
votes
5
replies
845
views
Wig file interpreted as bed file in genome browser
Genome Browser
updated 3.1 years ago by
genecats.ucsc
▴ 570 • written 3.1 years ago by
salamandra
▴ 360
5
votes
6
replies
4.3k
views
Visualize bigwig, bedgraph, wig files on Genome Browser?
RNA-Seq
ChIP-Seq
Genome Browser
updated 3.1 years ago by
Buffo
★ 1.8k • written 3.1 years ago by
salamandra
▴ 360
0
votes
1
reply
772
views
USCS visualization track for genomic bins
ucsc
genome browser
visualization
updated 3.2 years ago by
max
▴ 40 • written 3.3 years ago by
cjgunase
▴ 30
2
votes
0
replies
1.1k
views
Job:
UCSC Genome Browser Software Engineer, University Of California, Santa Cruz, CA , USA
ucsc
genome browser
software engineer position
Job
3.3 years ago by
ann
▴ 40
1
vote
2
replies
2.3k
views
How to show my chosen SNPs on the UCSC genome browser?
SNP
genome browser
updated 3.3 years ago by
Biostar
20 • written 5.3 years ago by
1078256104
• 0
2
votes
2
replies
1.3k
views
Search set of SNPs on genome browser by rsid
genome
genome browser
updated 3.5 years ago by
Pierre Lindenbaum
135k • written 3.5 years ago by
lordoftheowl
▴ 10
4
votes
7
replies
1.5k
views
How to embed genome browser in a web site?
genome browser
updated 4.0 years ago by
cmdcolin
★ 1.5k • written 4.0 years ago by
biolab
★ 1.3k
6
votes
2
replies
1.9k
views
Tool:
UCSC Custom Track Generator Script
genome browser
visualization
Tool
updated 4.0 years ago by
David Langenberger
9.6k • written 4.0 years ago by
steve
★ 2.9k
2
votes
3
replies
883
views
Genome Browser and Custom Tracks
Genome Browser
Custom Track
4.1 years ago by
justinms
▴ 10
2
votes
9
replies
2.1k
views
csv into genome browser
SNP
genome browser
4.5 years ago by
H.Hasani
▴ 980
4
votes
6
replies
1.3k
views
6 follow
chromosomal cordinates of a list of genes
genome browser
updated 5.1 years ago by
Giovanni M Dall'Olio
27k • written 5.1 years ago by
bioguy24
▴ 220
1
vote
2
replies
1.8k
views
How can I make all tracks on genome browser always scale relative to each other?
genome browser
rnaseq
5.1 years ago by
tiago211287
★ 1.3k
8
votes
5
replies
1.3k
views
Genome browser for website (ASP.net)
asp.net
genome browser
variation
SNP
updated 5.2 years ago by
Jean-Karim Heriche
24k • written 5.2 years ago by
Whoknows
▴ 860
3
votes
6
replies
1.6k
views
Do wiggle files have to be sorted?
genome browser
wiggle
custom track
genome
updated 5.3 years ago by
Alex Reynolds
32k • written 5.3 years ago by
asperlea
• 0
2
votes
0
replies
1.2k
views
Forum:
Free Ensembl courses
ensembl
course
workshop
genome browser
Forum
5.3 years ago by
Emily_Ensembl
22k
5
votes
4
replies
1.8k
views
How to obtain and compare genomic coordinates from RepeatMasker output?
repeats
repeatmasker
genome browser
gbrowse
5.4 years ago by
gbdias
▴ 100
9
votes
8
replies
3.6k
views
Is there a "consumer" level genome browser?
genome browser
personal genomics
updated 5.4 years ago by
devonEnlis
• 0 • written 6.9 years ago by
Mary
11k
9
votes
13
replies
5.9k
views
Where can I find the coordinates of mitochondrial DNA on the human genome on UCSC Genome Browser?
mtDNA
DNA-Seq
coordinates
ucsc
genome browser
updated 5.8 years ago by
Jeremy Leipzig
20k • written 5.8 years ago by
quachtina96
▴ 40
3
votes
1
reply
1.8k
views
Link UCSC genome browser session with custom tracks
UCSC
genome browser
sillybilly
5.9 years ago by
QVINTVS_FABIVS_MAXIMVS
★ 2.4k
6
votes
6
replies
1.5k
views
Convenient way to visualise a collection of genomic locations
ChIP-Seq
visualisation
genome browser
updated 6.0 years ago by
Friederike
6.9k • written 6.0 years ago by
Saulius Lukauskas
▴ 540
1
vote
2
replies
2.1k
views
How to retrieve "UTR" sequence from "Exon" of "Canonical Transcript" from a list of gene symbols?
R
Genome Browser
BiomaRt
updated 6.2 years ago by
Devon Ryan
98k • written 6.2 years ago by
Hyun Jin
▴ 20
5
votes
13
replies
1.8k
views
Computational requirement to host a genome browser
genome browser
computational
updated 6.2 years ago by
Ian
5.7k • written 6.2 years ago by
CikLa
▴ 90
5
votes
3
replies
2.1k
views
Jbrowse: importance of draw-basepair-track.pl
jbrowse
genome browser
Forum
updated 6.3 years ago by
Mitch Skinner
▴ 660 • written 6.3 years ago by
CikLa
▴ 90
8
votes
6
replies
1.7k
views
Integrate a Genome Browser into a Java application
genome browser
igb
java
updated 6.3 years ago by
Ann
★ 2.3k • written 6.3 years ago by
pieromontanari3
▴ 20
4
votes
6
replies
6.0k
views
How to extract sequences from multz sequence alignment on UCSC genome browser?
genome browser
sequence alignment
updated 6.4 years ago by
Denise CS
★ 5.1k • written 6.4 years ago by
epigene
▴ 490
1
vote
0
replies
1.2k
views
visualization of multiz results from genome browser
sequence
alignment
mutliz
genome browser
6.8 years ago by
tomastokar
▴ 30
6
votes
2
replies
3.0k
views
Retrieve exon positions from UCSC Genome Browser
UCSC
Genome Browser
Exon
Positions
updated 6.8 years ago by
Michael Lawrence
▴ 100 • written 6.8 years ago by
QVINTVS_FABIVS_MAXIMVS
★ 2.4k
0
votes
5
replies
2.1k
views
Browser to display sequence searches in BAM files
BAM
nucleotide search
genome browser
6.8 years ago by
hyanwong
▴ 70
49 results • Page
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Recent Votes
A: Could you explain the difference between STAR, KALLISTO, SALMON etc. to experime
A: What the index means in illumina RNA-seq data file?
C: What is difference between bulk RNAseq and mRNAseq?
Answer: Taxonomy assignment of viral RNA
Answer: RNAseq data analysis of pooled data
Comment: RNAseq data analysis of pooled data
Answer: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
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Comment: Testing independence between 5' and 3' terminal sequences in a DNA database
by
Istvan Albert
87k
with that definition I would suspect that all of your sequences are "dependent", I would expect every functional DNA/RNA region to capture …
Comment: Taxonomy assignment of viral RNA
by
biobiu
▴ 120
Thanks! As for the blast option- (1) so do you suggest to just blast the contig against a db of viral RNAs? and (2) is there a comprehensiv…
Comment: Finding how many times a nucleotide appear in the same position
by
cpad0112
15k
#!/usr/bin/env python3 sequences = ["GAGGTAAACTCTG", "TCCGTAAGTTTTC", "CAGGTTGGAACTC", "ACAGTCAGTTCAC", "TAGGTCATTACAG", "TAGG…
Comment: Testing independence between 5' and 3' terminal sequences in a DNA database
by
Anand Rao
▴ 350
Thanks for your reply. Yes, I think I could have explained my problem much better, but rather than change my original post, I will add some…
Answer: Finding how many times a nucleotide appear in the same position
by
Dunois
▴ 600
Here's a little `python` function you can work off of: def count_quer_at_pos_in_seq(seqs, quer = "A"): #Initialize a list…
Comment: Using outgroup in gene family dendograms
by
Rogerio Ribeiro
▴ 50
Thank for the fast reponse. The ABC family is not the best example for this question indeed. The objective of my work is to find genes resp…
Answer: Taxonomy assignment of viral RNA
by
Zhilong Jia
★ 1.7k
1. Blast directly 2. [IDSeq][1], can get viral contigs and their annotation directly. [IDSeq : An open-source cloud-based pipeline and…
Comment: Finding how many times a nucleotide appear in the same position
by
hugo.avila
▴ 180
Hi, It is not a norm but it is a good practice to post an attempted resolution first and then other members try to correct it or suggest an…
Comment: What Do You Waste Your Time On
by
ponganta
▴ 150
Aye to the rushed analyses and the last-minute documentation. Horrible, but somehow it happens all the time.
Answer: What Do You Waste Your Time On
by
ponganta
▴ 150
Reinventing the wheel. Like, all the time. Why use clusterProfiler with an up-to-date GO-annotation, when you can just write your own clien…
Comment: RNAseq data analysis of pooled data
by
ponganta
▴ 150
By "pooled" data, do you mean data from tissue-specific bulk-RNAseq? Or did you pool single cell (SC) RNAseq-libraries?
Comment: RNAseq data analysis of pooled data
by
Dunois
▴ 600
What exactly do you mean by "pooled" data?
Answer: RNAseq data analysis of pooled data
by
grant.hovhannisyan
★ 2.1k
I made a tutorial last year for University students on this topic https://www.loom.com/share/a55c1dedb8e64e7cac47f6595b751de7. Let me know …
Comment: RNAseq data analysis of pooled data
by
luffy
• 0
@dunois Thank you for the tutorial, what are your thoughts for approach for pooled data? should i follow the documentation/the tutorial or …
Comment: How to extract only the specific fasta sequences by matching the ID's to a diff
by
pinn
▴ 90
In my case, it doesn't work. parallel --verbose 'echo "TRINITY_{}" > test__.txt | seqtk subseq /home/sunn/data/softwares/evaluation/Tr…
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