User: Andy

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Andy20
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Posts by Andy

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Picard tools - Cigar element being constructed with negative length
... Apologies for late reply. I don't get any output when I try the above command. Any ideas? Regards Andy ...
written 14 hours ago by Andy20
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Picard tools - Cigar element being constructed with negative length
... Hi I am trying to mine SNPs using Star 2-pass / GATK using the process outlined here. https://gatkforums.broadinstitute.org/gatk/discussion/3891/calling-variants-in-rnaseq I've run the two passes of STAR, but I'm getting an error during the picard processing step. When I run this command; ...
alignment rna-seq snp written 4 days ago by Andy20 • updated 14 hours ago by finswimmer6.7k
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Comment: C: What is the appropriate assembler for PacBio long reads
... There are numerous long-read assemblers available. Many listed here. https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbx147/4590140 ...
written 3 months ago by Andy20
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Comment: A: What protein database would you use to analyze soil samples [Metaproteomics]?
... If you want meaningful annotations, stick to SWISSPROT. NR isn't curated. I've not used it previously, but this tool is supposedly much faster than NCBI's BLAST. https://github.com/bbuchfink/diamond ...
written 3 months ago by Andy20
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Answer: A: Detecting Homozygous Insertion from Sanger Seq
... A heterozygous insertion will look like this; ![sanger electropherogram][1] [1]: https://www.gendx.com/SBTengine/Help/lib/imagesindel.gif A homozygous one will look like a regular electropherogram. ...
written 3 months ago by Andy20
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Comment: C: How can i run a local blastn on my denovo assemble (rnaseq data) for detection k
... Personally, I'd stick to the the swissprot database. NR isn't curated and will lead to a high proportion of misleading or meaningless annotations. ...
written 3 months ago by Andy20
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Comment: C: Tools for polyA site identification in DNA sequences
... At least some of the tools listed on the omictools site seem to work with DNA, including this one; https://omictools.com/dna-functional-sites-miner-tool and this one https://omictools.com/polyamotif-tool Are these not up to the task for some reason? ...
written 8 months ago by Andy20
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Comment: A: 10X Genomica Supernova Troubleshooting
... Peter.....could you also confirm whether these are Gemcoded reads made from a 10X Chromium library rather than any old Illumina data. I've recently been testing my system with the aphid genome to see it's up to the task before I apply it to my own data. 261M reads on the system you have ought to ...
written 8 months ago by Andy20
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Comment: A: 10X Genomica Supernova Troubleshooting
... Are you sure you have enough reads? The default setting is 1.2B (calculated for the 3.2 Gb human genome @ 57x coverage). You've only got around 11-fold coverage. Well below the recommended minimum of 38x. https://support.10xgenomics.com/de-novo-assembly/software/pipelines/latest/using/running ...
written 8 months ago by Andy20
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Answer: A: Workstations Built For Bioinformatics
... Don't join just to spam. ...
written 8 months ago by Andy20

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