User: yp19

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yp1950
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Posts by yp19

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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 21 hours 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 1 day 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 2 days 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 2 days 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 2 days 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 2 days 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 3 days ago by yp1950 • updated 2 days ago by predeus1.2k
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Comment: C: Understanding coverage in genome assemblies
... Every point on the plot is a scaffold. I always use a minimum of 500bp for scaffolds. ...
written 27 days ago by yp1950
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Allowing duplicates when matching values from two tables
... Hi all! I have a reference table of some pathway information that looks like this (rownames and first column are the same) [,1] [,2] PTHR11566:SF148 "PTHR11566:SF148" "INTERFERON-INDUCED GTP-BINDING PROTEIN MXA-RE ...
R written 6 weeks ago by yp1950 • updated 6 weeks ago by Chirag Parsania1.5k
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Comment: C: Family ID/Name in PANTHER
... Thank you. It appears that way. Just shocking that when I process it this way, almost 50% (47.6%) of family IDs have a blank family name. But I guess that's just what it is! ...
written 6 weeks ago by yp1950

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