Moderator: Darked89
Darked89 ♦ 4.1k
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Posts by Darked89
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... 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 21 months ago by
Darked89 ♦ 4.1k
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... 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 21 months ago by
Darked89 ♦ 4.1k
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... 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 21 months ago by
Darked89 ♦ 4.1k
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... 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 21 months ago by
Darked89 ♦ 4.1k
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... 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.
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written 22 months ago by
Darked89 ♦ 4.1k
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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 22 months ago by
Darked89 ♦ 4.1k
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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 22 months ago by
Darked89 ♦ 4.1k
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... 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 22 months ago by
Darked89 ♦ 4.1k
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... 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 22 months ago by
Darked89 ♦ 4.1k
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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 22 months ago by
Darked89 ♦ 4.1k
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