Moderator: Philipp Bayer

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Philipp Bayer6.4k
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PhilippBayer
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Post-Doc bioinformatics at the University of Western Australia, co-founder openSNP.org

Posts by Philipp Bayer

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Answer: A: Maker Annotation pipeline Output error
... Have you run the MAKER scripts `fasta_merge` to create the protein/transcript fasta files and `gff3_merge` to create the final gff file? ...
written 14 days ago by Philipp Bayer6.4k
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Answer: A: Annotation lifting to a different organism
... I *may* have a solution - I've had a similar error recently with an annotation that had many non-gene entries, i.e., snoRNAs, rRNAs, tRNAs etc. and those kept on causing problems in flo. After removing them all with this simple Python 3 script it worked fine (YMMV) bad_ones = set(['nCRNA','snoRNA' ...
written 16 days ago by Philipp Bayer6.4k
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Answer: A: A software tool for gene copy number and loss detection
... I've made good experiences with cn.MOPS: https://bioconductor.org/packages/release/bioc/html/cn.mops.html (which overlap quite a bit with a simplistic SGSGeneloss approach based on mosdepth and some scripting :) ) Hecaton is new and looking at the paper, it's quite exciting, but it's tailored at p ...
written 17 days ago by Philipp Bayer6.4k
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Comment: C: Annotation lifting to a different organism
... What does the output of /QRISdata/Q0231/apps/flo/gff_recover.rb run/TAIR10_GFF3_genes-fix1/lifted.gff3 | head say? ...
written 20 days ago by Philipp Bayer6.4k
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Answer: A: "ERROR:...Base position exceeds Integer.MAX_VALUE" using Refined IBD with map fi
... Integer.MAX_VALUE is a Java-internal hard-coded value, googling around it should be 2,147,483,647 on most systems - do you have base positions larger than that? ...
written 24 days ago by Philipp Bayer6.4k
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Answer: A: find orthology genes
... Looking at the hamstr code at https://github.com/BIONF/HaMStR/blob/master/bin/hamstr.pl, this error you're seeing: `"checking for presence of the hmm files:`, prints a few more lines to the log-file, NOT to the standard out: in case the hmmset is broken it writes this to the log file: push @l ...
written 4 weeks ago by Philipp Bayer6.4k
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Answer: A: Augustus output (GFF file) to Anvi`o
... I've made good experiences with this script: https://github.com/jorvis/biocode/blob/master/gff/convert_augustus_to_gff3.py when downstream software wasn't liking the AUGUSTUS gff3 (you'll have to run `pip install biocode` first) ...
written 5 weeks ago by Philipp Bayer6.4k
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Answer: A: Bias in GO enrichment analysis for non-model organsim?
... Yes, this is an important point that is often ignored in plant genomics papers! Here's a paper discussing GO database bias, with a bit on the bias imported by unannotated genes, but this is all in human: https://www.nature.com/articles/s41598-018-23395-2 The other problem is that most of your genes ...
written 5 weeks ago by Philipp Bayer6.4k
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Comment: C: Augustus Installation error
... `conda install boost` could solve this (perhaps then reinstalling augustus) ...
written 5 weeks ago by Philipp Bayer6.4k
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Comment: C: Augustus Installation error
... Seconding conda, if you don't want conda it's a common error message for which are numerous workarounds on the internet, see for example https://iamphioxus.org/2017/05/08/installing-augustus-with-manual-bamtools-installation/ (I also edited the code in the OP post) ...
written 5 weeks ago by Philipp Bayer6.4k

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