Moderator: Philipp Bayer

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Philipp Bayer6.6k
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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: Getting assembly from sam/bam file
... I think it's probably best if you use RaGOO for that - https://github.com/malonge/RaGOO It runs minimap2 using your contigs and a reference assembly and then orders the contigs based on the alignment. You may have to rerun your alignments, I don't know whether you can give it the sam file directly. ...
written 3 months ago by Philipp Bayer6.6k
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Comment: C: PLINK --allow-extra-chr error
... Have you tried using --allow-extra-chr without the 0? Have you tried looking at line 938485, 938486, 938487 to see whether these lines are just broken somehow? ...
written 4 months ago by Philipp Bayer6.6k
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Comment: C: Brassica napus reference genome
... Hi, here's a different fixed version: https://cloudstor.aarnet.edu.au/plus/s/hPwZU13L1Hx2nFM I re-added the missing gene-lines and sorted by chromosome and position ...
written 5 months ago by Philipp Bayer6.6k
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Comment: C: Brassica napus reference genome
... Hmmmm can't find it myself any more :O I got it on an old laptop? I'll re-create the file asap ...
written 5 months ago by Philipp Bayer6.6k
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Comment: C: Scaleable trimming of GenBank sequences?
... Amazing idea, I hadn't even thought of soft-clipping! I've currently written a relatively slow script that does what I describe in the OP post, after that I'll give BWA or similar a try, which is probably WAY faster, thanks for the idea!! Edit: FWIW, here's the simple script I ended up using - ran ...
written 5 months ago by Philipp Bayer6.6k
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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 5 months ago by Philipp Bayer6.6k
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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 5 months ago by Philipp Bayer6.6k
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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 5 months ago by Philipp Bayer6.6k
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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 7 months ago by Philipp Bayer6.6k
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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 7 months ago by Philipp Bayer6.6k

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