User: colindaven

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colindaven2.6k
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Staff Scientist Bioinformatics

Posts by colindaven

<prev • 429 results • page 2 of 43 • next >
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Answer: A: Programmatically retrieving taxon classification
... Have a look at https://github.com/shenwei356/taxonkit , I think it's exactly what you need ...
written 6 weeks ago by colindaven2.6k
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Answer: A: filtering alignned seqeunces
... A more standard way to do this would be 1. convert SAM to BAM with BAI index 2. run samtools idxstats x.bam 3. alternative: run samtools stats x.bam This would give you the stats including number of reads aligned to each reference as a text file. Very useful if you have many references. ...
written 7 weeks ago by colindaven2.6k
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Answer: A: how to parse a .fasta file in python ?
... Try biopython, from memory they use delimiters such as space to differentiate the ID from the name or annotation fields. It might be helpful to use sed etc in Linux to modify the fasta headers to get the ID and Name to "stick together", depending on what you want to do. You are right though, fasta ...
written 7 weeks ago by colindaven2.6k
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Comment: C: How to handle multiple contig outputs from de novo assemblers when one contig is
... If you have related genomes, potentially ref based scaffolding tools like this are useful. https://github.com/malonge/RaGOO https://github.com/combogenomics/medusa ...
written 10 weeks ago by colindaven2.6k
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Answer: A: Find repeat regions on 100 eukaryotic assemblies
... You can have a look at MAKER for annotation. https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-491 The DFAM database might help for data, but I don't know if that covers your insects. https://dfam.org/ Perhaps for large scale projects like this you need to apply for comput ...
written 10 weeks ago by colindaven2.6k
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Comment: C: Best open source genome browser in 2020
... I use the server version exclusively. It's not too hard to set up and you want your software where the data lives to avoid endless unnecessary data transfers. ...
written 10 weeks ago by colindaven2.6k
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Answer: A: Best open source genome browser in 2020
... I'm a big fan of JBrowse. I prefer it to the likes of IGB and IGV because of the much faster loading times for big BAMs. It also allows you to structure information for users so they can explore data integration. I haven't tried JBrowse2 yet, but its on my list and brand new in 2020. ...
written 11 weeks ago by colindaven2.6k
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Comment: C: RIP CentOS, CentOS 8 to be EOL'd in 2021
... We're running a ca 1000 core SLURM cluster on Ubuntu. The LTS are very good, docs are great. There's another cluster here running on RHEL but that's from IT. We had a look at Debian but far less docs, and even essential programs like ls can be subtly different. ...
written 11 weeks ago by colindaven2.6k
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Comment: C: Searching subreads used to assemble contig of interest (canu)
... You'll probably get a good answer on the canu github repo. ...
written 11 weeks ago by colindaven2.6k
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Answer: A: can i detect regulatory proteins with co-expression network?
... This post might be relevant for you: https://www.biostars.org/p/77756/ ...
written 11 weeks ago by colindaven2.6k

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