Moderator: Philipp Bayer

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Philipp Bayer6.8k
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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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Comment: C: Scaleable trimming of GenBank sequences?
... (A few minutes later: Current best pipeline I can find is MAFFT/MUSCLE with gaps turned off, followed by trimAl, in a wrapper script to parallelise? curious to hear more!) ...
written 10 months ago by Philipp Bayer6.8k
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Scaleable trimming of GenBank sequences?
... I'm trying to automate the building of a reference database for DADA2. As such I'm using esearch to download ~200k fasta sequences for my search term of one gene from GenBank. Many GenBank sequences are joined-up sequences of several genes, and I'd like to trim those unnecessary genes away in order ...
alignment written 10 months ago by Philipp Bayer6.8k
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Answer: A: Difficulties in Trinity installation
... I think if you install Trinity via conda or if you use the Singularity or Docker images provided you can circumvent this problem. What is the output of `which salmon`? That's what Trinity runs to check for your salmon installation. There's a chance that the salmon in /usr/bin/ isn't set to executab ...
written 10 months ago by Philipp Bayer6.8k
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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 12 months ago by Philipp Bayer6.8k
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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 12 months ago by Philipp Bayer6.8k
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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 12 months ago by Philipp Bayer6.8k
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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 13 months ago by Philipp Bayer6.8k
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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 months ago by Philipp Bayer6.8k
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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 15 months ago by Philipp Bayer6.8k
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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 15 months ago by Philipp Bayer6.8k

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Good Answer 13 days ago, created an answer that was upvoted at least 5 times. For A: New To Python And Putty: Help!
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Scholar 4 weeks ago, created an answer that has been accepted. For A: Long reads Assembly Algorithms
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Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Directions In Bioinformatics And Web-Based Data Visualization: Revisiting Javasc
Popular Question 3 months ago, created a question with more than 1,000 views. For How does MAKER decide which proteins go into the final output?
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Appreciated 6 months ago, created a post with more than 5 votes. For A: New To Python And Putty: Help!
Popular Question 9 months ago, created a question with more than 1,000 views. For How does MAKER decide which proteins go into the final output?
Scholar 9 months ago, created an answer that has been accepted. For A: Long reads Assembly Algorithms
Scholar 9 months ago, created an answer that has been accepted. For A: Long reads Assembly Algorithms
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Scholar 11 months 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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Popular Question 15 months ago, created a question with more than 1,000 views. For How does MAKER decide which proteins go into the final output?
Scholar 16 months 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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