User: dylan.lawrence

Reputation:
10
Status:
New User
Location:
Last seen:
3 days, 20 hours ago
Joined:
1 year, 2 months ago
Email:
d*************@wustl.edu

Posts by dylan.lawrence

<prev • 24 results • page 1 of 3 • next >
0
votes
2
answers
112
views
2
answers
Comment: C: Convert list of Accession Numbers to Full Taxonomy
... Is there a general database? My accessions have a huge number of prefixes. ...
written 14 days ago by dylan.lawrence10
1
vote
2
answers
112
views
2
answers
Convert list of Accession Numbers to Full Taxonomy
... I swear this question has been asked and never satisfyingly answered for over a decade. I know the simplest answer is to perform a bunch of Entrez queries, but to quote many infomercials, "There's got to be a better way." Here's the setup, I have a file of straight accession numbers extracted fr ...
ncbi taxonomy accession numbers written 14 days ago by dylan.lawrence10 • updated 14 days ago by genomax63k
0
votes
0
answers
349
views
0
answers
Comment: C: aligning to circular sequence
... Have you considered [Circlator?][1] [1]: https://sanger-pathogens.github.io/circlator/ ...
written 5 months ago by dylan.lawrence10
0
votes
0
answers
389
views
0
answers
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 8 months ago by dylan.lawrence10
0
votes
0
answers
389
views
0
answers
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 8 months ago by dylan.lawrence10
0
votes
0
answers
298
views
0
answers
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 8 months ago by dylan.lawrence10 • updated 3 months ago by Biostar ♦♦ 20
0
votes
1
answer
256
views
1
answers
Comment: C: Generating Web BLAST output from local BLAST
... I did not know there was an html flag option. Thank you! ...
written 10 months ago by dylan.lawrence10
2
votes
1
answer
256
views
1
answer
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 10 months ago by dylan.lawrence10 • updated 10 months ago by Pierre Lindenbaum117k
0
votes
0
answers
478
views
0
answers
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 12 months ago by dylan.lawrence10
0
votes
0
answers
2.0k
views
0
answers
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 13 months ago by dylan.lawrence10

Latest awards to dylan.lawrence

Popular Question 5 months ago, created a question with more than 1,000 views. For Best command line ORF finder

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2166 users visited in the last hour