Moderator: genomax

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genomax49k
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Posts by genomax

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Comment: C: What is the definition of "multiply aligned" sequences compared to multiple alig
... 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 genomax49k
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Comment: C: plasmid assemby from Illumina reads - help!
... Excellent. I moved my comment to an answer. Feel free to accept it to provide closure for this thread. ...
written 7 hours ago by genomax49k
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Comment: C: What is the definition of "multiply aligned" sequences compared to multiple alig
... `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 genomax49k
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Comment: C: Retrieve PubMed records based on some genes
... 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 genomax49k
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Answer: C: plasmid assemby from Illumina reads - help!
... > 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 genomax49k
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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 genomax49k
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Comment: C: How to improve single-cells data ?
... > 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 genomax49k
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Comment: C: BigWig from ensembl assembly to UCSC session
... Perhaps they are unaware of the option to view these at Ensembl. Any chance of suggesting this option? ...
written 12 hours ago by genomax49k
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Answer: A: BigWig from ensembl assembly to UCSC session
... 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 genomax49k
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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 genomax49k

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