Moderator: genomax
genomax ♦ 49k
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Posts by genomax
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... Based on the publication you linked that would be a sequence aligned to an existing multiple-sequence alignment (where differences would be expressed as regular expressions). I will need to look at the paper more closely to be sure. ...
written 6 hours ago by
genomax ♦ 49k
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... Excellent. I moved my comment to an answer. Feel free to accept it to provide closure for this thread. ...
written 7 hours ago by
genomax ♦ 49k
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... `Multi-mapped sequences` are those reads that can equally map well in multiple locations in a reference. You can think of repeat regions which can allow this (especially if the reads are much shorter than the actual repeats).
`Multiplexing` is adding index sequences to fragments from a sample (one ...
written 7 hours ago by
genomax ♦ 49k
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... I am going to make some general comments.
You will want to use `OR` instead of `AND` in your terms since I don't get any hits with all three genes in the example above with `AND` when using NCBI eUtils. A ton of hits appear, if the terms are used individually or combined with `OR`. What is your ult ...
written 8 hours ago by
genomax ♦ 49k
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... > 1x150
Is that accurate? Or was it a paired-end run and was actually `2x150`?
You may want to normalize read coverage (if you have a lot of it, which is known to cause problems with assembly). Take a look at `tadpole.sh` [guide here][1] and `bbnorm.sh` [guide here][2].
[1]: https://jgi.doe ...
written 8 hours ago by
genomax ♦ 49k
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Answer:
A: h38 total genes ?
... GENCODE has [a statistics page][1] for this information.
[1]: https://www.gencodegenes.org/stats/current.html ...
written 11 hours ago by
genomax ♦ 49k
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... > I have to improve pretty bad single cells data (~10/20% of coverage
> against the genome reference of the species in question
That is about what people get from `drop-seq` which is a technique for single cell expression data. Are you working with plain DNA sequence? ...
written 11 hours ago by
genomax ♦ 49k
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... Perhaps they are unaware of the option to view these at Ensembl. Any chance of suggesting this option? ...
written 12 hours ago by
genomax ♦ 49k
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... If you used Ensembl assembly for analysis then why not use [custom tracks feature][1] at Ensembl to view the data?
Note: Chromosomal identifier styles are different between UCSC and Ensembl so this is not going to work on UCSC without additional work.
[1]: https://www.ensembl.org/info/website/u ...
written 12 hours ago by
genomax ♦ 49k
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Comment:
C: GTF file for HIV strain pNL4-3
... If you have the genbank file you could try using a genbank2gtf type program to make one up. Here is [one repo][1].
[1]: https://github.com/riverlee/genbank2gtf ...
written 13 hours ago by
genomax ♦ 49k
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