User: shelkmike
shelkmike • 130
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Posts by shelkmike
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... First of all, thank you. ALAPY compressor has helped our laboratory to reduce the size of sequencing reads made by our HiSeq a lot. What I want to ask: could you please make an option to decompress many files by one command? Like "alapy_arc -d *.ac" instead of "alapy_arc -d some_single_file.ac". It ...
written 5 months ago by
shelkmike • 130
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... Frankly speaking, I don't understand the purpose of what you do. You have the sequence of a genome, you split it into k-mers, and then assemble these k-mers to produce contigs of this genome. What for, if you already have the sequence of this genome?
Could you explain the purpose of your analysis? ...
written 6 months ago by
shelkmike • 130
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... A quote from Masurca's configuration file:
"MUST HAVE Illumina paired end reads to use MaSuRCA".
So, there is no way to do what you want.
Almost all other assemblers are able to do what you want, you just need to give these k-mers to them as single-end reads. By the way, why do you do an assembly f ...
written 6 months ago by
shelkmike • 130
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... If I have understood correctly, you are speaking about two orthogroups, which are descendants of a pair of paralogs in the last common ancestor of the studied species. Each species has one gene from each of the two orthogroups. The tree you provide to PAML should not be the species phylogenetic tree ...
written 6 months ago by
shelkmike • 130
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... By indels I mean not genomic variants, but sequencing errors which result in insertion or deletion of a sequence in a sequencing read compared to the genome. ...
written 6 months ago by
shelkmike • 130
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... Thank you once again. Sorry for doubts, but if nothing mentions it, how do you know that probabilities of indels are not reflected in FASTQ in some way? ...
written 6 months ago by
shelkmike • 130
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... Thank you. Also, can you give a link to a source where I can read about this? ...
written 6 months ago by
shelkmike • 130
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... Try to replace "~" with a full path to the reads ...
written 6 months ago by
shelkmike • 130
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... How many single copy orthogroups you get depends on how phylogenetically distant your species are (the more distant, the less single copy orthogroups you will have) and also on how good the genome assemblies are. Based on my experience, 78 single orthogroups is not bad. This may be enough to create ...
written 6 months ago by
shelkmike • 130
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... Could you please clarify what "my one species tree won't work" means? ...
written 6 months ago by
shelkmike • 130
Latest awards to shelkmike
Scholar
6 months ago,
created an answer that has been accepted.
For A: Criteria for filtering contigs after spades assembly
Popular Question
8 months ago,
created a question with more than 1,000 views.
For Is BUSCO really better than CEGMA for genome assembly quality evaluation?
Scholar
18 months ago,
created an answer that has been accepted.
For A: Criteria for filtering contigs after spades assembly
Supporter
2.9 years ago,
voted at least 25 times.
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