Moderator: Philipp Bayer

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Philipp Bayer6.5k
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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: Problems with SRA: curl: (9) Server denied you to change to the given directory
... I've had this recently too, where the official ftp didn't have a file the European or UK counterpart had. Sometimes the raw fastq works then: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR197/009/SRR1972739/SRR1972739_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR197/009/SRR1972739/SRR1972739_2 ...
written 6 weeks ago by Philipp Bayer6.5k
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Comment: C: publicly available data
... One avenue would be to check the SRA. Many, not all, BioProjects have a DOI of the paper they're associated with, so you could get the BioProject associated with the abstract without scanning the paper! ...
written 8 weeks ago by Philipp Bayer6.5k
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Answer: A: SSD or HHD for genome analisys
... Interestingly, there's a whole paper about this! https://academic.oup.com/bib/article/17/4/713/2240499/ It looks like some programs sped up significantly, others had no improvement. Personally I'd rather go for space than for speed (so the 2x2TB HDD), but I work with massive plant genomes, I don't ...
written 9 weeks ago by Philipp Bayer6.5k
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Answer: A: Putting R codes on MS word document
... You can write your whole analysis in Markdown including your code blocks, and then render it into Word and back using redoc: https://github.com/noamross/redoc ...
written 3 months ago by Philipp Bayer6.5k
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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 4 months ago by Philipp Bayer6.5k
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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 4 months ago by Philipp Bayer6.5k
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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 4 months ago by Philipp Bayer6.5k
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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 4 months ago by Philipp Bayer6.5k
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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 4 months ago by Philipp Bayer6.5k
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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 months ago by Philipp Bayer6.5k

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Scholar 9 days ago, created an answer that has been accepted. For A: Quickest way to extract subset of reads from huge fastq file
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