User: effidotpy

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effidotpy10
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Posts by effidotpy

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Comment: C: Parsing psiblast xml with BioPython
... You are right, there is no 'round' in the xml, but there is not either an 'alignments' node and yet I can get it from the record. I assume the NCBIXML parser reads the xml and assigns the xml nodes to objects of the `Bio.Blast.Record.Blast` or `Bio.Blast.Record.PSIBlast` class. These classes and the ...
written 4 days ago by effidotpy10
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Comment: C: Parsing psiblast xml with BioPython
... Thank you for your response Pierre. Sure, you can look at or download it [here][1]. [1]: https://gofile.io/d/dJeI1Q ...
written 4 days ago by effidotpy10
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Parsing psiblast xml with BioPython
... Hi there, I'm trying to use BioPython to parse the xml output generated by psiblast (local execution, -outfmt 5). I aim to identify each of the 'iteration round', which should be one of the attributes of the `Bio.Blast.Record.PSIBlast` class, so I can extract the information for the last iteration ...
parse biopython psiblast written 4 days ago by effidotpy10
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Comment: C: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remov
... Thanks [genomax][1], truly helpful as always. [1]: https://www.biostars.org/u/18713/ ...
written 3 months ago by effidotpy10
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Comment: C: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remov
... I agree about PCR duplicates arising during library prep, but then what about the optical ones? Should be removed? Sorry but I find all of this duplicates thing a bit confusing. I have read several good threads like this one itself or [this][1] among others, and I thought optical should be removed, ...
written 3 months ago by effidotpy10
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Comment: C: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remov
... I'm a bit confused with the [you should not be deduplicating RNAseq data in normal cases][1] sentece. I'm working with stranded RNAseq data coming from Novaseq to perform differential expression analysis, and I actually removed optical duplicates (dedupe=t, dupedist=12000. 3-4% of reads were removed ...
written 3 months ago by effidotpy10
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Comment: C: Snakemake flow variantion
... Your help did the trick. Thanks mates! Regarding your question russhh, I want to use this "switch" for the whole experiment, i.e to process all its samples equally. The point is that I also want to use this workflow for another experiments that might require some extra intermediary steps. ...
written 5 months ago by effidotpy10
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Snakemake flow variantion
... Hi, I have been able to create my own linear workflows (A -> B -> C -> D) with Snakemake. However, now I would like to include some optional steps (X) that should be only executed if the user specifies it. Briefly, most of the times C will take as input the output from B, but sometimes I wo ...
python workflow snakemake automatization written 5 months ago by effidotpy10 • updated 5 months ago by russhh5.5k

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