User: el97004

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el9700410
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Posts by el97004

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Comment: C: Interpret genome alignment results
... Thank you that makes sense. But how about in less extreme case scenarios, for example if the third codon in the DNA is mutated it could have no affect on the protein sequence ...
written 2 days ago by el9700410
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Comment: C: Interpret genome alignment results
... Sorry I should have clarified. Whole genomes! ...
written 2 days ago by el9700410
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Interpret genome alignment results
... Hi all! I assembled two different genomes and wanted to see how similar they are on both nucleotide and protein levels so I aligned their nucleotide and translated nucleotide sequences. Here are the results I obtained: Nucleotide identity=90% Protein identity=57% How would one make sense of this ...
nucleotide alignment protein written 3 days ago by el9700410 • updated 2 days ago by michael.ante3.5k
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Comment: C: Assembly statistics: abyss & bbmap
... Thanks! I tried all values of n between 1-10 but unfortunately cannot get the same number of contigs as in abyss (=997), the closest I got was 970 at n=1. Edit: I wonder if the contig statistics are off because I am using the scaffolds file as input to BBmap stats.sh..what if this is the only file ...
written 5 days ago by el9700410
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Comment: C: Assembly statistics: abyss & bbmap
... Thanks for your reply, https://www.biostars.org/u/50123/. I think I know how to solve the second item you mention (I will filter for scaffolds > 500 bp and re reun BBmap `stats.sh`), for the first item, do you know what I should modify this value to in BBmap `stats.sh` so that it matches that of ...
written 5 days ago by el9700410
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Assembly statistics: ABySS & BBMap
... Hi! I have noticed some differences in resulting assembly statistics from Abyss and BBMap stats.sh and was wondering if anyone knew why. For example, this is an output I get from Abyss: n n:500 L50 min N80 N50 N20 E-size max sum name 3854 1282 71 500 2119 17327 40129 23269 ...
assembly bbmap abyss written 6 days ago by el9700410
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Comment: C: Query coverage in global alignment
... Unfortunately **-awidth3** does not do it. However as I am thinking more about this problem, perhaps query coverage does not really make sense for global alignments since they are trying to align proteins from end to end, so i think % query cover in a global alignment may just be the same as the % i ...
written 13 days ago by el9700410
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Comment: C: Query coverage in global alignment
... Thanks! I will give that a try. ...
written 13 days ago by el9700410
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Comment: C: Query coverage in global alignment
... Hi https://www.biostars.org/u/22207/ , I am referring to query coverage in sequence alignments not sequencing depth. From Blast documentation: The query cover is a number that describes how much of the query sequence is covered by the target sequence. This tells us how long the sequences are, relati ...
written 14 days ago by el9700410
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Query cover in global alignment
... Hi, Does anyone know how I can modify the command line parameters in needleall to output query coverage? So far my code below only gives me values for Identity, similarity, gaps, and score. needleall -asequence proteins_f1.fa -bsequence proteins_f2.fa -outfile needle_results -aformat pair -ga ...
global alignment needleman coverage written 14 days ago by el9700410 • updated 12 days ago by gb1.0k

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