User: cschu181

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Posts by cschu181

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Comment: C: Kallisto: Impact of chosen reference transcriptome on the resulting TPMs
... You could also try and run salmon or sailfish or ... on both sets and see if that results in similar tpm differences. ...
written 4 days ago by cschu1812.1k
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Comment: C: Is there any tools for detecting Kinase Domain Duplication?
... Just a thought on this: I'd assume that you could treat the reference genes with single kinase domains as kind of a collapsed assembly of the diseased genotype. A duplication could then be reflected by increased coverage of the original domains in the reference genes. ...
written 4 days ago by cschu1812.1k
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Comment: C: Kallisto: Impact of chosen reference transcriptome on the resulting TPMs
... Jeez....oh come on ><; ...
written 4 days ago by cschu1812.1k
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Comment: C: Kallisto: Impact of chosen reference transcriptome on the resulting TPMs
... I am not 100% sure if this affects pseudoalignment methods such as kallisto, but with traditional aligners, you might misalign reads to a close enough reference sequence if their actual origin is not included in the reference. You'll always have that risk when using reduced reference sets, so I'd sa ...
written 4 days ago by cschu1812.1k
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Comment: C: Single amino acid in a .pdb file and torsion angles
... > Is it possible to have just one amino acid in a .pdb file? Right now I was going the unsophisticated way of simply deleting every amino acid except the first one from a already existing .pdb file, but I'm afraid that this will corrupt the .pdb file. Yes it is possible. The "PDB file" is just ...
written 4 days ago by cschu1812.1k
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Comment: C: Centrifuge - Error: reads file does not look like a FASTQ file
... Shouldn't that be `nufile=$(echo $file | cut -d '_' -f 1)`? ...
written 8 days ago by cschu1812.1k
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Comment: C: INDELs frequency at the on-target site in CRISPR experiment
... I think you can do that with CRISPResso, but it's been a while... ...
written 12 days ago by cschu1812.1k
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Answer: C: How to translate protein sequences to Nucleotide sequences?
... As lieven.sterck points out: this returns you 'a' backtranslation of a peptide sequence. You could use a more dedicated statistical model using codon frequencies from your organism under study, but this is the gist of it: import random AA2NA = { "A": list("GCT,GCC,GCA,GCG".spli ...
written 15 days ago by cschu1812.1k
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Comment: C: Generation of neighbourhood words in blast
... Maybe OP doesn't know conda :D. But seriously, I think it's a great thing to try and (re-)build things such as blast. Not necessarily for production purposes, but I think this is the best way to understand how things work (and with that, hone one's skill set). Of course, one could say 'read the blas ...
written 19 days ago by cschu1812.1k
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Comment: C: DNA Codon Table vs RNA Codon Table?
... Same as above, you'd use the DNA table only when working on the cDNA level or in case of single-exon genes. You could transcribe, but in any case other than cDNA / single-exon, this would cause intron content to be transcribed, which would then result in a mistranslated protein product (frameshifts ...
written 21 days ago by cschu1812.1k

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