User: dylan.lawrence

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Posts by dylan.lawrence

<prev • 18 results • page 1 of 2 • next >
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Comment: C: Generating Web BLAST output from local BLAST
... I did not know there was an html flag option. Thank you! ...
written 4 weeks ago by dylan.lawrence10
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Generating Web BLAST output from local BLAST
... Is it possible to generate the web page for blast results from a local blast? I find all the command line blast output to be difficult to read, particularly for what I am doing. ...
blast written 4 weeks ago by dylan.lawrence10 • updated 4 weeks ago by Pierre Lindenbaum108k
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Local BLAST+ search very slow
... I am blasting several assembled contigs from IDBA-UD with lengths between 13,000 and 250bp. BLAST+ seems to be taking a very long time to achieve this. I am using a local `nt` database and the job should have plenty of memory (25Gb). If I take this same file and use the web based BLAST portal it tak ...
contig blast written 3 months ago by dylan.lawrence10
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Comment: C: Best command line ORF finder
... How exactly do I download getORF... I have looked all over the website and it is not obvious to me where it is. ...
written 3 months ago by dylan.lawrence10
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Best command line ORF finder
... I am currently using the NCBI Orf Finder website which works great, but I want to automate my pipeline a bit more and am trying to find a good command line based Orf Finder. I tried to download the NCBI version but they only provide a pre-compiled version which the server I use is a missing a librar ...
software orf command line written 3 months ago by dylan.lawrence10
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Comment: C: Algorithms to know when starting out analyzing transcriptome data
... BLAST is the biggie. Got sequences, first step is probably to BLAST them. ...
written 4 months ago by dylan.lawrence10
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Comment: C: kraken: unable to download the databases from ncbi
... Are you able to download anything from the NCBI ftp server using `wget`? ...
written 4 months ago by dylan.lawrence10
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Comment: C: heterozygosity during variant calling in a non-model organism such as Bubalus Bu
... I am not entirely sure how to interpret that particular paper's SNP frequencies but you may be able to compare that paper to this paper on human heterozygosity and get a good benchmark; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3586588/ There also may not be a consensus in your field and the bes ...
written 4 months ago by dylan.lawrence10
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Comment: C: heterozygosity during variant calling in a non-model organism such as Bubalus Bu
... I do not know anything specific about Bubalus bubalis but the question to ask here is how you are performing the variant calls. I assume there's a reference genome? Are there multiple. An important question is whether previous studies generating Bubalus bubalis genomes have found any statistics on h ...
written 4 months ago by dylan.lawrence10
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Comment: C: Kraken failing to map reads when reads are merged.
... This is the full set of reads, we got between 150,000 and 250,000 demultiplexed reads. This was spike-in data and it is mostly just a "what's there" type of thing. We are actually trying to do FACS on bacteria and wanted to test a computational method for making sure we have single bacteria, but the ...
written 5 months ago by dylan.lawrence10

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