User: robert.murphy

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Posts by robert.murphy

<prev • 53 results • page 1 of 6 • next >
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Culture independent detection of bacterial biosynthetic gene clusters from microbiomes
... I am wanting to identify biosynthetic gene clusters present in various bacterial microbiomes surrounding the host I work with. Previous efforts have used metagenomic approaches which has always resulted in highly fragmented MAG due to low sequencing depth of bacterial reads because of to much host ...
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Normalization of raw Illumina reads.
... I am looking for an optimal method for de novo assembly of fungal isolates and came across this [nice nature paper][1]. They use a combination of methods and in two of them (workflow 2 and 3) they mention normalization of the data: > To overcome MDA-generated differences in coverage across the ...
assembly sequencing written 11 days ago by robert.murphy10 • updated 11 days ago by RamRS30k
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Comment: C: SPAdes v3.14 unable to find files despite correct file path
... I am slurm so yes. How can I ensure the node has the file path? If the node does not then how come `echo $fwd` prints the expected output to the stdout ...
written 21 days ago by robert.murphy10
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Comment: C: Is it possible to supplement a gbk file with manual annotations?
... Thank you very much :) I think i will trey use biopython to read in the existing gbk and edit it with new annotations ...
written 25 days ago by robert.murphy10
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Comment: C: Is it possible to supplement a gbk file with manuall annottions?
... So I can just write a script to manually insert the annotations as the desierd location? Would this be eaiser in a GFF file? ...
written 25 days ago by robert.murphy10
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Is it possible to supplement a gbk file with manual annotations?
... I have a viral genome gbk file that only shows the open reading frame, I wish to also annotate each ORF with the 5' and 3' UTRs that have been published in a paper so I have the coordinates in a table but I want to annotate these onto the gbk file. Is there a tool that can do this and if not, how ca ...
genome annotation viral written 25 days ago by robert.murphy10 • updated 25 days ago by Mensur Dlakic6.9k
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Comment: C: SPAdes v3.14 unable to find files despite correct file path
... using just {} gives the same error `metaspades.py -1 ${fwd} -2 ${rvs} -o ${outdir}` ...
written 25 days ago by robert.murphy10
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Comment: C: SPAdes v3.14 unable to find files despite correct file path
... Tried in command line and it runs correctly. I seems to remember having this error another time with spades but can't remember the cause ...
written 25 days ago by robert.murphy10
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Comment: C: SPAdes v3.14 unable to find files despite correct file path
... I have added the commands ...
written 25 days ago by robert.murphy10
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Comment: C: SPAdes v3.14 unable to find files despite correct file path
... I have added the commands ...
written 25 days ago by robert.murphy10

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