Moderator: Darked89

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Darked894.2k
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Posts by Darked89

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Comment: C: Q:Data files naming schemes
... I have tried that route, but got stuck at the downstream data processing. Meaning: if one does not implement the entire Broad pipeline, I still have to parse ubam's say RG info myself. Also being on the slow net I tend to shrink the data with clumpify from BBMap and pigz/pbzip2. I need to check if u ...
written 5 weeks ago by Darked894.2k
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Q:Data files naming schemes
... I am getting a piles of fastq files with either generic (R12345.r1.fq) or plainly confusing (170811p1pt.r1.fq). While storing md5, project name etc. helps a bit, I feel that without a massive scale rename I will not be able to make a sense of the results, or even get the results in the first place. ...
sequencing written 5 weeks ago by Darked894.2k • updated 5 weeks ago by Pierre Lindenbaum124k
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Comment: C: Genotyping by sequencing in Arundo donax
... 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 4.1 years ago by Darked894.2k
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Answer: A: Genotyping by sequencing in Arundo donax
... 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 4.1 years ago by Darked894.2k
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Comment: C: Genotyping by sequencing in Arundo donax
... 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 4.1 years ago by Darked894.2k
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Answer: A: Recommended data warehouse tools for bioinformatics search?
... 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 4.1 years ago by Darked894.2k
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Comment: C: Aligning BAC to an assembled sequence
... 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 4.1 years ago by Darked894.2k
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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 4.1 years ago by Darked894.2k • updated 1 day ago by RamRS24k
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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 4.1 years ago by Darked894.2k
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Comment: C: Aligning BAC to an assembled sequence
... 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 4.1 years ago by Darked894.2k

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