Moderator: Darked89
Darked89 ♦ 4.2k
- Reputation:
- 4,190
- Status:
- Trusted
- Location:
- Barcelona, Spain
- Website:
- http://openwetware.org...
- Last seen:
- 13 hours ago
- Joined:
- 8 years, 8 months ago
- Email:
- d**********@gmail.com
Posts by Darked89
<prev
• 284 results •
page 1 of 29 •
next >
0
votes
2
answers
1.3k
views
2
answers
... If these are based on 1.8% mapped reads to Setaria genome, I would try to get more reads mapped first. At this mapping rate you will be looking at differences between your mutants in some special regions only.
If you really must, check where these SNPs/indels are located intersecting VCF with Setar ...
written 3.1 years ago by
Darked89 ♦ 4.2k
1
vote
2
answers
1.3k
views
2
answers
... re mapping genomic DNA to transcriptome: I would try LAST http://last.cbrc.jp/ because with any read spanning the intron-exon border more mainstream mappers I believe will reject the mapping because of the mismatch (intronic sequence from the read vs next exon in your transcript). LAST, given reason ...
written 3.1 years ago by
Darked89 ♦ 4.2k
1
vote
2
answers
1.3k
views
2
answers
... Interesting problem. But some vital IMHO data is missing:
how large is the genome and what is the level of polyploidy?
do you sequence with enough coverage to discover any of the changes?
what are the expected mutations & mutation rates caused by the radiations you have used? Similar to on ...
written 3.1 years ago by
Darked89 ♦ 4.2k
1
vote
3
answers
1.2k
views
3
answers
... Unless you need something really extraordinary in terms of presenting the genomic data, abandon the idea of writing such system from scratch, especially as a first step.
Use Jbrowse, collect opinions, and if end users really need more, then rather invest your time into installing a local copy if EN ...
written 3.1 years ago by
Darked89 ♦ 4.2k
1
vote
1
answer
1.5k
views
1
answers
... Here we go (Shameless self-plug mode on):
http://openwetware.org/wiki/Wikiomics:WinterSchool_day2#last
One can do this MAF to BAM coversion not just with mapped short reads but also with contigs/BAC sequences or other genomes. And verify some tricky spots by eye if necessary.
...
written 3.1 years ago by
Darked89 ♦ 4.2k
0
votes
0
answers
1.1k
views
0
answers
Comment:
C: compiling clustalx executables
... Happy that it did work for you. If you need to know how the clustalx is being compiled, you may look around at Debian:
https://tracker.debian.org/pkg/clustalx
Also depending how trivial is the alignment task, you may check mafft & t-coffee.
...
written 3.1 years ago by
Darked89 ♦ 4.2k
1
vote
0
answers
1.1k
views
0
answers
Comment:
C: compiling clustalx executables
... Are you installing some super-duper development version of ClustalX? Because you can save time and effort by doing
sudo apt-get install clustalx
The Ubuntu version is 2.1 (see below) so there is nothing really to gain by compiling ver 2.1 from source:
http://packages.ubuntu.com/precise/clustalx ...
written 3.1 years ago by
Darked89 ♦ 4.2k
0
votes
1
answer
1.5k
views
1
answers
... There are two LAST utilities: maf-swap and maf-cull. What you can do is to swap top (scaffolds from db) sequence with a contigs seq from your BAC(s). Then cull all the hits except the top one.
If you are into assembly checking/scaffold building, look also in LAST as a short read mapper (map reads ...
written 3.1 years ago by
Darked89 ♦ 4.2k
1
vote
1
answer
1.5k
views
1
answers
... You may try to use LAST: http://last.cbrc.jp/
First create database from your assembly, then query it with your BAC fasta. You will get MAF output you can parse.
Caveat: repetitive contigs may be dropped from the output. But then it may be the correct behavior: Imagine that your BAC insert in real ...
written 3.1 years ago by
Darked89 ♦ 4.2k
0
votes
1
answer
891
views
1
answers
Comment:
C: process substitution input
... I assume you are using DiscoSNP? Check this post: https://www.biostars.org/p/156901/
Not that by some magic program authors implemented random access to gz files...
...
written 3.1 years ago by
Darked89 ♦ 4.2k
Latest awards to Darked89
Great Question
13 months ago,
created a question with more than 5,000 views.
For Taxonomy Of Blast Hits
Good Question
13 months ago,
asked a question that was upvoted at least 5 times.
For Taxonomy Of Blast Hits
Popular Question
13 months ago,
created a question with more than 1,000 views.
For parsing BAM index (quick&dirty samtools view X.bam region)
Appreciated
2.4 years ago,
created a post with more than 5 votes.
For A: Aligning Two Proteins With Their Domains/Annotations
Popular Question
2.4 years ago,
created a question with more than 1,000 views.
For parsing BAM index (quick&dirty samtools view X.bam region)
Great Question
2.4 years ago,
created a question with more than 5,000 views.
For Taxonomy Of Blast Hits
Scholar
2.4 years ago,
created an answer that has been accepted.
For A: Best Hardware Solution For Medium-Size Bioinformatics Lab [15-20 Computers]
Popular Question
2.4 years ago,
created a question with more than 1,000 views.
For Ests Cleanup: Seqclean Alternatives?
Popular Question
2.5 years ago,
created a question with more than 1,000 views.
For Taxonomy Of Blast Hits
Great Question
2.7 years ago,
created a question with more than 5,000 views.
For Taxonomy Of Blast Hits
Popular Question
2.8 years ago,
created a question with more than 1,000 views.
For Taxonomy Of Blast Hits
Epic Question
2.9 years ago,
created a question with more than 10,000 views.
For Gff3 + Fasta To Genbank (Augustus Training Set)
Popular Question
3.0 years ago,
created a question with more than 1,000 views.
For Taxonomy Of Blast Hits
Popular Question
3.0 years ago,
created a question with more than 1,000 views.
For Gff3 + Fasta To Genbank (Augustus Training Set)
Great Question
3.1 years ago,
created a question with more than 5,000 views.
For Taxonomy Of Blast Hits
Popular Question
3.1 years ago,
created a question with more than 1,000 views.
For Taxonomy Of Blast Hits
Commentator
3.2 years ago,
created a comment with at least 3 up-votes.
For C: Change Coordinates -A 1.Bam -B 2.Bam -O 3.Bam?
Epic Question
3.8 years ago,
created a question with more than 10,000 views.
For Sam Format Parsing / Stats
Popular Question
3.8 years ago,
created a question with more than 1,000 views.
For Taxonomy Of Blast Hits
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1853 users visited in the last hour