Moderator: Charles Warden

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Charles Warden8.0k
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I am a Bioinformatics Specialist at City of Hope, where I work in the Integrative Genomics Core doing microarray and high-throughput sequencing analysis.

However, the feedback that I provide represent my own personal opinions.

Posts by Charles Warden

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Arrow GFF Does Not List All Polishing Changes
... Hi, I was considering using the GFF file produced by arrow to transfer annotations before and after polishing. However, I noticed that this file does not contain a full list of changes made by polishing. This means the strategy above can have problems. For example, here is an Arrow polishing GFF ...
arrow gff polishing pacbio written 6 weeks ago by Charles Warden8.0k
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Comment: C: Transferring Gene Annotations from Assembly with Large Duplications
... While it didn't help for this specific project, there is also some additional discussion about the parameters to create a .chain file for liftOver / CrossMap here: https://groups.google.com/a/soe.ucsc.edu/g/genome-mirror/c/zx665aZPEXU ...
written 8 weeks ago by Charles Warden8.0k
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Answer: A: Transferring Gene Annotations from Assembly with Large Duplications
... I have also written some code to map coordinates based upon a **.pileup file created from a BWA-Alignment** (of the new sequence to the old sequence). I don't think this will work if there are any inversions or complex structural variants. However, I think this may be OK if you **just need to shif ...
written 8 weeks ago by Charles Warden8.0k
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Comment: C: Transferring Gene Annotations from Assembly with Large Duplications
... I am not sure how much it helps, but there is some additional background about this task here: https://github.com/marbl/canu/issues/1841 ...
written 8 weeks ago by Charles Warden8.0k
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Comment: C: Transferring Gene Annotations from Assembly with Large Duplications
... Also, to provide a bit more justification for this strategy (even though it still isn't perfect and I would encourage additional feedback), I thought it might help to add some screenshots: A couple examples for one class of gene: ![YF example 1][1] ![YF example 2][2] An example for a different c ...
written 9 weeks ago by Charles Warden8.0k
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Answer: A: Transferring Gene Annotations from Assembly with Large Duplications
... I was a bit surprised, but I think the protein query with `protein2genome` worked better than the coding query with `coding2genome` (even though different CDS sequences can produce the same protein). Similar to my other answer, I used the `--percent 97 --maxintron 2000` parameters. GffCompare stati ...
written 9 weeks ago by Charles Warden8.0k
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Answer: A: Transferring Gene Annotations from Assembly with Large Duplications
... It is not a complete answer, but adding ` --maxintron 2000` helped clean up that outlier gene. In the current test example, adding `--percent 97 --maxintron 2000` doesn't seem to remove any additional hits, but the first loss of some hits for this example occurs with a changing the threshold from 9 ...
written 9 weeks ago by Charles Warden8.0k
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Transferring Gene Annotations from Assembly with Large Duplications
... I would like to transfer some gene annotations between a previous and updated assembly (for 1 “chromosome,” derived from what was originally a circular BAC). There will be a mix of large and small changes in the underlying sequence. I think this is difficult because there are exact and non-exact d ...
assembly exonerate maker liftover annotation written 10 weeks ago by Charles Warden8.0k
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Comment: C: the best combine score for enrichment analysis from Enrichr
... You probably already realize this, but the z-score represents something different in IPA: http://pages.ingenuity.com/rs/ingenuity/images/0812%20upstream_regulator_analysis_whitepaper.pdf I think there was some simplified version of the IPA z-score that I could calculate to (approximately) verify, ...
written 10 weeks ago by Charles Warden8.0k
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Comment: C: the best combine score for enrichment analysis from Enrichr
... ***UPDATE***: I am not sure if this is what I meant before, but I tested trying to calculate what the z-score should be (as the combined score / ln(unadjusted p-value)). I noticed that this matches the negative odds-ratio. The numbers are so close that I don't think it is a coincidence. This is a ...
written 11 weeks ago by Charles Warden8.0k

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