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User: shelkmike

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shelkmike • 130
Reputation:
130
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Trusted
Location:
Russian Federation
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Last seen:
2 days, 18 hours ago
Joined:
5 years, 5 months ago
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Posts by shelkmike

<prev • 22 results • page 1 of 3 • next >
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Answer: A: Do all samples in SRA have a corresponding sample in BioSample?
... According to the rules of NCBI, it is mandatory for each SRA submission to have a registered corresponding BioSample: "Registering project and biological samples at the NCBI BioProject and the BioSample databases is a prerequisite for any public SRA submission" (https://www.ncbi.nlm.nih.gov/sra/docs ...
written 4 months ago by shelkmike • 130
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Comment: C: Lossless ALAPY Fastq Compressor (now for MacOS X with 10-20% improved speed and
... 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 10 months ago by shelkmike • 130
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Comment: C: How to use a single file as the input to MaSuRCA
... 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 11 months ago by shelkmike • 130
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Answer: A: How to use a single file as the input to MaSuRCA
... 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 11 months ago by shelkmike • 130
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Answer: A: How do you run codeml for two genes in one file but with 1 species tree?
... 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 11 months ago by shelkmike • 130
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Comment: C: How are probabilities of insertions and deletions encoded in FASTQ?
... 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 11 months ago by shelkmike • 130
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Comment: C: How are probabilities of insertions and deletions encoded in FASTQ?
... 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 11 months ago by shelkmike • 130
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Comment: C: How are probabilities of insertions and deletions encoded in FASTQ?
... Thank you. Also, can you give a link to a source where I can read about this? ...
written 11 months ago by shelkmike • 130
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Answer: A: masurca invalid forward file for PE library
... Try to replace "~" with a full path to the reads ...
written 12 months ago by shelkmike • 130
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Answer: A: problem with SingleCopyOrthogroups
... 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 12 months ago by shelkmike • 130

Latest awards to shelkmike

Voter 22 days ago, voted more than 100 times.
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Phylogeny from incomplete orthogroups
Scholar 11 months ago, created an answer that has been accepted. For A: Criteria for filtering contigs after spades assembly
Popular Question 13 months ago, created a question with more than 1,000 views. For Is BUSCO really better than CEGMA for genome assembly quality evaluation?
Scholar 24 months ago, created an answer that has been accepted. For A: Criteria for filtering contigs after spades assembly
Supporter 3.3 years ago, voted at least 25 times.
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