User: yp19

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yp1950
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Posts by yp19

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Comment: C: protein databases with GI numbers
... Yes that is true, however I'm trying to run a tool that requires gi numbers as part of the input ([Horizontal gene transfer tool][1]) Is there anyway around this? [1]: http://alienness.sophia.inra.fr/cgi/index.cgi ...
written 16 hours ago by yp1950
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protein databases with GI numbers
... Hi all, Anyone know whether NCBI (or any other website) has a protein database that includes GI numbers for each protein? I have read that they have become obsolete in the NCBI nr database as of a few years ago, and when I blastp against the nr database I do not see them as part of the output. T ...
ncbi database nr protein blastp written 20 hours ago by yp1950
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MUMmer overall identity & output
... Hi guys! I want to use nucmer to assess how similar two species' assemblies are to one another. I used the command like this: nucmer sp1_scaffolds.fa sp2_scaffolds.fa --coords and in the output I get a series of alignment records with the following columns [S1] [E1] | [S2] [E2] | [L ...
species mummer nucmer written 3 months ago by yp1950
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Comment: C: Sequence duplication levels in de-novo assemblies
... The number of sequences did go down. The second sentence (%seqs remaining if deduplicated) is referring to the value produced in the fastQC sequence level duplication plot (I re ran fastQC post clumpify). Since some of the duplicated reads were removed, we get a higher % of sequences remaining on th ...
written 4 months ago by yp1950
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Comment: C: Sequence duplication levels in de-novo assemblies
... Awesome, thank you for the link! To update: I ran clumpify to remove optical and PCR duplicates and in each case only a small % of reads were removed. The % of seqs remaining if deduplicated increased ~15% in each case (from ~42-57%) ...
written 4 months ago by yp1950
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Comment: C: Sequence duplication levels in de-novo assemblies
... Thanks! could you briefly explain the difference between the two duplicates (i.e. optical vs. PCR) as I don't think I understand it. Also is it possible that I am seeing this high level of duplication due to the high degree of coverage? ...
written 4 months ago by yp1950
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Comment: C: Sequence duplication levels in de-novo assemblies
... It seems like the duplication is there after mapping as well. Thanks for your suggestions I will try out MarkDuplicates and Genomescope to get a better understanding of the data. ...
written 4 months ago by yp1950
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Comment: C: Sequence duplication levels in de-novo assemblies
... Thanks! Yes, it took out the duplications. Although, I went from ~19 million (paired) reads to ~2million post normalizing. The command I used was: bbnorm.sh in=samp.fq.gz out=normalized.fq.gz target=100 min=5 ...
written 4 months ago by yp1950
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Comment: C: Sequence duplication levels in de novo assemblies
... Thanks for your suggestion. I tried this out. Only problem is, my assembly statistics are worse after normalization (N50 is decreased by more than half), so I am tempted to avoid this step. Any other suggestion for dealing with this high level of duplication? ...
written 4 months ago by yp1950
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Sequence duplication levels in de-novo assemblies
... Hi all! Is such a result ( https://imgur.com/DGxsFN7 ) concerning if the overall goal is to do de-novo genome assembly? I continued with the data as is, assembled and predicted proteins and I did find that some proteins were duplicated (not sure if this is caused by what we see above?) anyways I t ...
de-novo fastqc duplication written 4 months ago by yp1950 • updated 4 months ago by predeus1.3k

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