Moderator: Philipp Bayer
Philipp Bayer ♦ 4.8k
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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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... SPAdes runs its own read data trimming and error correction so you don't have to do that.
However it's still highly advisable to run adapter trimming, for example using Trimmomatic. Torsten Seeman also has a pipeline around SPAdes called shovill which has a --trim option which will run Trimmomatic ...
written 3 hours ago by
Philipp Bayer ♦ 4.8k
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... [Prokka][1]!
[GitHub link][2]
It's easy to use, is often updated, makes all usual files in formats ready for submission to Genbank
[1]: http://www.vicbioinformatics.com/software.prokka.shtml
[2]: https://github.com/tseemann/prokka ...
written 1 day ago by
Philipp Bayer ♦ 4.8k
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Answer:
A: linear genome visualization
... Normally AliTV should pick up its own Perl packages, strange.
You can manually add other modules like this:
export PERL5LIB=/data/ngs/programs/AliTV-perl-interface/lib/AliTV/Alignment:$PERL5LIB
That will tell Perl where the missing lastz.pm is. It may then complain about other missing modul ...
written 3 days ago by
Philipp Bayer ♦ 4.8k
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... You get this strange circle since you have many, many scaffolds, and you get alignments for all of those tiny circles. The black ring is the names of all scaffolds.
You can't really run this kind of approach with scaffolds, it makes much more sense to run it pseudomolecule by pseudomolecule. You ca ...
written 12 days ago by
Philipp Bayer ♦ 4.8k
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... Just like you I've run into problems with that file! Two years ago I made a sorted/fixed version of the v5 annotation, I just put it here: https://www.dropbox.com/s/i7r90w6qn8tno90/Brassica_napus_annotation_v5_fixed_sorted.zip?dl=0
Not sure whether this version works with your RNASeq pipeline, if n ...
written 16 days ago by
Philipp Bayer ♦ 4.8k
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Answer:
A: Faster version of STRUCTURE
... fastSTRUCTURE has been released 3 years ago: https://rajanil.github.io/fastStructure/
Paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4063916/
Takes binary PLINk files (bed/bim/fam) as input, I've had good success with it (definitely much faster than STRUCTURE but I have no numbers right now) ...
written 19 days ago by
Philipp Bayer ♦ 4.8k
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... I haven't heard back anything, but just going over the middle step of using the returned ID works ...
written 21 days ago by
Philipp Bayer ♦ 4.8k
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... Aah I see - have you tried removing all lines where there are indels, i.e., where the ALT field has more than one letter (here: ACTA)? I don't think 23andMe has those ...
written 21 days ago by
Philipp Bayer ♦ 4.8k
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... That doesn't look like a vcf file to me -
'multi-char alleles' appear when you have more than one alternative allele, which should be impossible if it's for a single human like 23andMe files are. Are you sure your example is your vcf file?
It should look like:
##fileformat=VCFv4.0
##fileD ...
written 21 days ago by
Philipp Bayer ♦ 4.8k
2
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... First, you'd have to change your sequences so that the DNA is all in one line, without this step you'd miss possible motifs hits that have line breaks in them.
From Pierre Lindenbaum: https://www.biostars.org/p/9262/#9264
awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);} END {prin ...
written 21 days ago by
Philipp Bayer ♦ 4.8k
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