Admin: genomax

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genomax91k
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Posts by genomax

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Comment: C: Trimming P5 and P7 dual index adapters (and other QC)
... My apologies. Should have said `trimpolyg=15` or you can also try `filterpolyg=5`. Using `literal=GGGGGGGG` should work as well. Unless you are going to do `de novo` work you can probably ignore the poly-G. Those reads should not align to anything. ...
written 3 days ago by genomax91k
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Comment: C: Archive GenomeStudio projects?
... While someone may answer you may want to email Illumina tech support and ask. Post their answer here once you hear back from them. ...
written 3 days ago by genomax91k
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Answer: A: hCoV-229 genome fa file
... At [NCBI][1]. Click on "Fasta" near top and then send to a "File" to save locally. [1]: https://www.ncbi.nlm.nih.gov/nuccore/12175745 ...
written 3 days ago by genomax91k
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Comment: C: Note for Biostar moderators
... Simply inserting a link (needs to be public gist) `https:// gist.github.com/your_user_name/random_number` should be enough. Biostars code will render it automatically. ...
written 3 days ago by genomax91k
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Answer: A: Note for Biostar moderators
... There are some known problems with code parsing (especially with parenthesis in specific instances, also with python code) and there is no immediate solution. You can host the code in a GitHub `gist` and link that here. https://gist.github.com/genomax/4b99f319b3e2b562f5343edd6cfd3267 Biostars wil ...
written 3 days ago by genomax91k
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Comment: C: BLAST search with multile fasta sequences and with a single output
... > I have tried a large dataset about 600,000ESTs and it resulted in 900 > sequences. What does that mean? Only 900 sequences generated results or you got a total of 900 hits for all these queries. If you truly have EST's and a reference genome then you should consider using a specialized ali ...
written 3 days ago by genomax91k
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Comment: C: Duplication rate differs up to 30% from that of Fastqc for single end reads
... Fastqc does not look at your entire dataset (I don't know about `fastp`) when it checks read duplication. It only uses sequences which first appear in the first 100,000 sequences in each file for this module. While this is generally representative of data it looks like they may not be in your case ( ...
written 3 days ago by genomax91k
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Comment: C: Trimming P5 and P7 dual index adapters (and other QC)
... Poly-G's are clusters with no signal. This must be data from a 2-color sequencer. You can also remove the poly-G's by using option `trimpolyg=0`. ...
written 3 days ago by genomax91k
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Comment: C: Rust or C++, what to learn after Go for high-performance bioinformatics tools?
... Certain folks on Biostar slack are fans of `rust` (@Rob Patro, @Wouter). `c++` will make you generally marketable (though you probably have enough skills not to need that). ...
written 3 days ago by genomax91k
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Comment: C: Samtools view error:
... See if this applies: https://github.com/samtools/samtools/issues/1237 ...
written 4 days ago by genomax91k

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