Moderator: Philipp Bayer

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Philipp Bayer4.8k
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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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Answer: A: Quality trimming for denovo assembly
... 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 Bayer4.8k
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Answer: A: What is the most usefull and up to date Prokaryotic Genome annotation Pipeline?
... [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 Bayer4.8k
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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 Bayer4.8k
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Answer: A: Very strange circle from MCScanX
... 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 Bayer4.8k
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Answer: A: Brassica napus reference genome
... 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 Bayer4.8k
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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 Bayer4.8k
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Comment: C: Entrez API returns results different from main search?
... 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 Bayer4.8k
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Comment: C: How to convert vcf to 23andme format
... 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 Bayer4.8k
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Answer: C: How to convert vcf to 23andme format
... 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 Bayer4.8k
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Answer: A: about Grep the complete sequences containing a specific motif in a fasta file
... 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 Bayer4.8k

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