User: dylan.lawrence

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Posts by dylan.lawrence

<prev • 21 results • page 1 of 3 • next >
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Comment: C: PacBio assemblies only ending up somewhere between 80 and 250 contigs.
... Not in depth but I have performed Illumina sequencing on this same sample and there were no contaminants. ...
written 5 weeks ago by dylan.lawrence10
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PacBio assemblies only ending up somewhere between 80 and 250 contigs.
... I have done a lot of denovo assembly with NGS data (Illumina NextSeq and MiSeq) and expect to only get a "pretty good" final assembly. However with PacBio I was under the impression this improved greatly. I'm struggling to finalize assemblies though. Currently I have tried the following assemblers: ...
de novo assembly pacbio written 5 weeks ago by dylan.lawrence10
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Issues running pbsmrtpipe and confirmation dialogue
... I am trying to perform de novo assembly using HGAP on PacBio SMRT sequencing using the `smrttools` package. I am currently running this command: pbsmrtpipe pipeline-id pbsmrtpipe.pipelines.polished_falcon_fat -e eid_subread:prefix.subreadset.xml --preset-xml preset.xml However we have discove ...
pacbio written 7 weeks ago by dylan.lawrence10
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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 3 months 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 3 months ago by dylan.lawrence10 • updated 3 months ago by Pierre Lindenbaum111k
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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 5 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 6 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 6 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 6 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 6 months ago by dylan.lawrence10

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