User: Atu

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Atu0
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Posts by Atu

<prev • 12 results • page 1 of 2 • next >
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Answer: A: Converting HGVS cDNA notations to chromosome position
... There are several libraries to work with hgvs ids. You may check the hgvs python library for mapping IDs to genomic coordinates: http://hgvs.readthedocs.org/en/0.4.x/reference.html ...
written 5.0 years ago by Atu0
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Answer: A: FastQC Results -- Per Sequence GC Content and Kmer Contents
... I think you should assess carefully the quality of your data, and if all the other modules are OK a think data is still valuable. It's a pity you can't show graphs. By post-mapping duplicate removal you could deal with the issue of duplications, and about the other two... How was DNA fragmented, by ...
written 5.0 years ago by Atu0
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Comment: C: Please help with removing spaces from fasta file
... Yes, any trailing character will be removed (white spaces plus newline character), but newline characters will be added again by the print fuction. So the output FASTA should be well-formed. Happy New Year! ...
written 5.1 years ago by Atu0
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Answer: A: Please help with removing spaces from fasta file
... Hi, I think you could make use of the python `rstrip()` string method. Just call it while reading your fasta file, and it will handle the the white spaces as you want. for line in open('path_to_fasta_file'): print line.rstrip() Copy the code into a file, say my_script.py, and run ...
written 5.1 years ago by Atu0 • updated 13 months ago by _r_am32k
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Comment: C: GFA to Fasta file
... Hi, could you describe what does GFA stand for? I don't know about this format. ...
written 5.1 years ago by Atu0 • updated 13 months ago by _r_am32k
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Comment: C: How is determined the exact length of a gap on a genome assembly?
... Thanks for your answer! ...
written 5.1 years ago by Atu0
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Comment: C: How is determined the exact length of a gap on a genome assembly?
... Hi. Yes, I was thinking on the human reference. I guess it is a genome deeply studied and that there will be several information sources, but I don't know how do they determined the exact length in bp of a gap, or the exact length in bp of a chromosome. Thanks ...
written 5.1 years ago by Atu0 • updated 13 months ago by _r_am32k
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How is determined the exact length of a gap on a genome assembly?
... Hi everyone, I was wondering how is known orgiven the length of a gap in a genome assembly. Thanks ...
gaps assembly scaffolds written 5.1 years ago by Atu0 • updated 5.1 years ago by h.mon32k
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Comment: C: HGMD accession number meaning
... Thanks for you answer. ...
written 5.2 years ago by Atu0
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HGMD accession number meaning
... Hi, I want find out what do the the prefix string in a HGMD accession number mean. I write down the prefix of the accession numbers I've seen and my guess after my search. Does anybody know something about this? Are they meaningless? 'CI'  -> Insertion. Coding. 'CM' -> Substitution. Coding. ...
myposts written 5.2 years ago by Atu0 • updated 5.2 years ago by stensonpd70

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