User: Ahill
Ahill • 1.2k
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Posts by Ahill
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... The chromsome X sequence was assembled from genomic DNA fragments that were packaged into fosmids. In this case, your fosmid (FO081428.1) was one of a number of fosmids that were assembled together to form the inferred chromosome X sequence (NC_003284.9). So this is not a contamination - in fact t ...
written 11 days ago by
Ahill • 1.2k
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... You mentioned you are running on a linux cluster. What job management system are you using? How many fastq files (elements in ${cells[@]})? If more than one,can you simply unroll your for loop, which runs each $cell serially, and execute a set of simultaneous jobs that will run in parallel, one p ...
written 4 weeks ago by
Ahill • 1.2k
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... The longer list of 6007 genes shown at the link you provided appears to include multiple other phenotypes and species, and an export filtered to "Homo sapiens" yields 10,396 genes, which makes me question the interpretation of this interface. You may want to query the site owners or their documenta ...
written 4 weeks ago by
Ahill • 1.2k
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... I'll add that one consideration driving the number of probe-pairs per probe-set in later Affymetrix designs was the desire to query more transcripts in the same amount of silicon real estate, given the fixed size (in square microns) of each probe feature, which was determined by the resolution of th ...
written 5 weeks ago by
Ahill • 1.2k
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... Have you tried contacting Thermo software technical support? For this type of error, in a commercial software package, they might be your best bet. Generally, the Thermo Omics software portal at [http://portal.thermo-brims.com][1] has sometimes offered helpful information in the past (for Proteome ...
written 6 weeks ago by
Ahill • 1.2k
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... Guessing an EC2 free tier micro instance is unlikely to meet your needs for genome-scale BAM analysis. As academics, are you perhaps eligible for free credits at [AWS][1] or [Azure][2] that could get you started.
[1]: https://aws.amazon.com/education/awseducate/
[2]: https://azure.microsoft. ...
written 9 weeks ago by
Ahill • 1.2k
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... Interested if others are aware of more direct methods, but have you looked at [this post][1], which uses BioPython to process an alignment?
Using the same approach, if you can output your Kalign 2.0 alignment in any format supported by [BioAlignIO][2], you could write a short script to iterate thro ...
written 9 weeks ago by
Ahill • 1.2k
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... Per:
https://www.ebi.ac.uk/arrayexpress/help/accession_codes.html
E-MTAB = Experiments in MAGE-TAB format, submitted via the MTAB spreadsheet submission tool (retired in September 2014), or via Annotare
E-MEXP = EBI MIAMExpress webform submission tool (deprecated since July 2014)
...
written 5 months ago by
Ahill • 1.2k
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... Depending on the content of the Bruker file, probably yes. For MSn spectra the MGF format is just a series of fragment ion masses with optional intensities, surrounded by BEGIN IONS and END IONS, as described [here][1]. So if your Bruker ASCII file has fragment ion masses, then you could translate ...
written 6 months ago by
Ahill • 1.2k
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For A: Why gene expression data should be log2 transformed?
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For A: Why gene expression data should be log2 transformed?
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For C: So what counts as a "novel" classifier?
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