User: colindaven

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colindaven2.4k
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Staff Scientist Bioinformatics

Posts by colindaven

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Comment: C: bacterial genome assembly with nano pore sequence data
... The read length is critical for genome assembly. Check the read lengths of both datasets. I find the tool stats.sh from the bbmap package to be an excellent tool for this (it's actually intended for checking assembly contig stats but works well for long reads too). Also, which assembler are you ...
written 4 days ago by colindaven2.4k
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Comment: C: Suggestion for tools to data transfer
... Maybe a proxy is blocking the FTP if you're behind an institutional firewall. Can you access the remote FTP from another computer, eg at home, and copy to external hard disks ? Syncthing is very nice on local networks, I use it at home to sync laptop, mobile and pc. ...
written 4 days ago by colindaven2.4k
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Answer: A: Inside a .sam file, how do I know which read maps where to which scaffold in the
... Looks like this one : NODE_1_length_3415511_cov_137.721502 Check the SAM spec for further details! https://samtools.github.io/hts-specs/SAMv1.pdf ...
written 5 days ago by colindaven2.4k
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Answer: A: Aligning & Comparing References for SNPs / Indels
... Have a look at pairwise tools like Mummer which can give you an optimal alignment. The file formats are somewhat ... strange ... though. By that I mean they are difficult to process further. I would also look at multiple genome alignment (i.e. all six at once). Mugsy is one tool which works, and yo ...
written 8 days ago by colindaven2.4k
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Comment: C: error: BAM to FASTQ
... Try remapping your BAM (which aligner did you use?). It looks to be corrupted/incorrect as the header does not contain reference chromosome lines. samtools view -h BAMFILE | less ...
written 8 days ago by colindaven2.4k
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Comment: C: Having made a paired-end and stranded-forward sequencing (NGS) implies that I wi
... For de novo assembly, if not already completed, try Trinity. Then you can use the tool transdecoder on your contigs to predict ORFs and get protein seqs etc. ...
written 9 days ago by colindaven2.4k
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Answer: A: Getting reference genome for vcf2maf tool
... As far as I understand this https://docs.cancergenomicscloud.org/docs/tcga-grch38-data then it should be the GDC version here: https://gdc.cancer.gov/about-data/gdc-data-processing/gdc-reference-files Have you tried that ? ...
written 14 days ago by colindaven2.4k
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Answer: A: Rust or C++, what to learn after Go for high-performance bioinformatics tools?
... I'm a big fan of rust. The way it pulls in crates and makes a binary after compilation (great for cluster environments) is very impressive. It's a lot more modern than C++ in my estimation, but as you said not easy to learn. ...
written 15 days ago by colindaven2.4k
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Answer: A: while running ONT(nanopore) bioinforamtics pipeline, fasta files are not generat
... I think you need to clear up the terminology you're using a bit - MinKNOW is the control software for Minion. I think this is what you mean when you say Minion. It can now be used for alignment, which I think is what you've been doing to generate BAM and VCF. As a side note, you can generate FASTQ ...
written 20 days ago by colindaven2.4k
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Comment: C: Extend 3' UTR of a GTF file
... Nope, I have not heard of anything like this, so your approach seems reasonable. I only know of Portcullis which deals with correcting fake alternative splice sites from RNA-seq. I think there are a couple of typos in your description which might improve understanding. Cheers for posting this scrip ...
written 29 days ago by colindaven2.4k

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Popular Question 9 days ago, created a question with more than 1,000 views. For Using the MinION MinKNOW software on Ubuntu 1604
Scholar 5 weeks ago, created an answer that has been accepted. For A: Gene annotation pipeline for bacteria
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