User: colindaven

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colindaven830
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Hannover Medical School
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Posts by colindaven

<prev • 164 results • page 1 of 17 • next >
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Answer: A: How to perform SOAPdenovo for many samples
... #!/bin/bash for i in `ls *.fastq` do soapdenovo2 $i & done You'll need to set up the config files for each separately though but try that. Otherwise try something like Abyss which doesn't need a config file. ...
written 1 day ago by colindaven830
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Comment: C: ChIP-Seq for viral genomes
... I think your analysis is correct, and the tools are optimised for large genomes. Never had to do small genome chip-seq analysis, thankfully. I think careful manual curation is appropriate in this case. One thing that has really helped me in Chip-seq analysis is using the Mulitbamsummary tools then ...
written 1 day ago by colindaven830
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Comment: C: ChIP-Seq for viral genomes
... Not really answering your question, but I'd be concerned with cross contamination to the host (human?) genome. I would definitely do the short experiment of adding your virus genome to the human genome and then aligning all reads and redoing the MACS analysis. I bet there are a few false positive ...
written 5 days ago by colindaven830
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Answer: A: Second assembly from existing contigs
... Theres a tool called metassembler which might help you out. https://github.com/biol7210-genomes/assemblers/blob/master/metassembler.md However, it's a difficult and inherently biased undertaking. I'd try to pick the two most complete assemblies for use. I.e. #2 and #4 Actually, #2 looks pretty ...
written 6 days ago by colindaven830
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Comment: C: How can I assembly big genome by abyss with 128 Gb ram
... I wouldn't divide up the fastq. Soapdenovo2 might be more memory efficient for you. Minia certainly will be, but assemblies are poor in my experience. Good luck. If you're really struggling and those tools don't work I could perhaps run assemblies for you if you gave me the exact commands to run ...
written 6 days ago by colindaven830
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Comment: C: Nanopore only assembly errors
... Sounds like you have done everything right. There is a lot known about P. aeruginosa and heaps of phylogeny information. If you can't do additional Illumina seq to correct the indels (that number of indels, i.e. 30% is the worst I've heard) maybe you can use public Illumina reads from an almost iden ...
written 19 days ago by colindaven830
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Answer: A: ABySS path setup for temporary files
... You can monitor the process with the following tools - gotop - htop - glances These should be easily installable under Ubuntu. But please state your server specs ! - RAM - hard disk space 140m PE illumina sequences will require a significant amount of mem and HDD space. I would guess at 6 ...
written 19 days ago by colindaven830
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Comment: C: Nanopore only assembly errors
... This sounds too high. - Which genome ? Prok/Euk? Size ? - How many rounds to nanopolish polishing ? - Which assembler was used? - Are the indels in reading frames? ...
written 21 days ago by colindaven830
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Comment: C: elPrep 4.0.0, a high-performance drop-in replacement tool for GATK4/Picard/SAMto
... Nonetheless, it's a nice tool and it's great people are trying to speed up bioinformatics infrastructure akin to what is going in the commercial and semi-commercial world with DRAGEN, MPEG-G and so on. So I will test a bit on Illumina X10 and NextSeq data I have and give feedback on any bugs I encou ...
written 21 days ago by colindaven830
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Comment: C: Reference database for shotgun metagenomics
... You're right to be sceptical. I have spent a long time working in and around this area. In any rate, it is a lot more robust than 16S. Nonetheless, I would always assess bacterial shotgun metagenomes with multiple tools and databases. Also, BLAST analysis can be helpful. Finally, controls are incre ...
written 22 days ago by colindaven830

Latest awards to colindaven

Voter 10 months ago, voted more than 100 times.
Centurion 10 months ago, created 100 posts.
Scholar 11 months ago, created an answer that has been accepted. For A: Gene annotation pipeline for bacteria
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Gene annotation pipeline for bacteria
Scholar 13 months ago, created an answer that has been accepted. For A: Best way to compare two samples in a VCF file
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Gene annotation pipeline for bacteria
Appreciated 21 months ago, created a post with more than 5 votes. For A: Gene annotation pipeline for bacteria
Scholar 21 months ago, created an answer that has been accepted. For A: Best way to compare two samples in a VCF file
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Gene annotation pipeline for bacteria
Scholar 23 months ago, created an answer that has been accepted. For A: Best way to compare two samples in a VCF file
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