Moderator: Philipp Bayer
Philipp Bayer ♦ 6.4k
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- PhilippBayer
- Last seen:
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- Joined:
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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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... 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 Bayer ♦ 6.4k
1
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... 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 Bayer ♦ 6.4k
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128
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... 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 Bayer ♦ 6.4k
0
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1
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... 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 Bayer ♦ 6.4k
0
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1
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... 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 Bayer ♦ 6.4k
0
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147
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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 Bayer ♦ 6.4k
0
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1
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120
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... 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 Bayer ♦ 6.4k
0
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1
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112
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... 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 Bayer ♦ 6.4k
0
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0
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148
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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 Bayer ♦ 6.4k
0
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0
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148
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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 Bayer ♦ 6.4k
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