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Recent Replies
Answer: ABySS genome assembler
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shelkmike
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You can use Kmergenie (http://kmergenie.bx.psu.edu/). It is a special tool for finding the optimal k-mer length.
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It is pretty trivial to do the COSMIC annotation without tools such as VEP - download their coding and non-coding VCFs, normalize (decompos…
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Figured I need to attach an expected OUTPUT result. Should look something like this:
----------
```
LOCUS 19 58617616 bp DNA HTG 23-NOV-2…
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Yes, well... surely it's better with some FPs and TPs than nothing at all, eh. Is there another way to do this? Hmm...
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No. All of the Ids are "13.02.1402_POOL2". Do you think my bam file is not correct?
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Yes, you're right, I know the bam file consists of multiple samples (It should be between 30 to 40 samples) and the size of the bam file is…
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Technically you can mask it, but what if the variant comes from the pseudogene and not the gene you "want"?
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Here is the simple guide for [Javascript][1], if you would like to give it a look.
[1]:
[1]: https://techindetail.com/javascript/
Answer: Retrieving allele-specific information for a variant using VEP annotation
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My interpretation of the documentation is that no, you can't have the specific COSMIC id, because of that licensing whatchamacallit.
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Hello Meisam. Understood! thank you
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https://github.com/kater…
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You should be filtering on field 5 in SAM file that is for mapping quality (MAPQ). As noted above any read that is multi-mapped should have…
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It is not clear what you mean by "neither provided me with the understandable results". Do they give you error? Then what error. Do they gi…
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A GTF file should not be a table unless you mean it in a loose sense. It should be a file with lines containing tabular fields. At a minimu…
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> I am now thinking that my PC's 16 Gb RAM is not enough
That is more than likely. See: https://www.biostars.org/p/295032/#295238
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