User: robert.murphy

gravatar for robert.murphy
Reputation:
10
Status:
New User
Location:
Last seen:
1 day, 20 hours ago
Joined:
2 months, 2 weeks ago
Email:
r************@bio.ku.dk

Posts by robert.murphy

<prev • 30 results • page 1 of 3 • next >
0
votes
0
answers
52
views
0
answers
Comment: C: Scanpy vs DeSeq for single cell RNASeq DE gene analysis
... These links are very useful but are all about analysis, I think my misunderstanding is in the differences between bulk RNAseq and scRNAseq. I have previously looked but been unable to find a recourse to inform me on this. However it also appears the main differences are actually in the analysis. but ...
written 1 day ago by robert.murphy10
1
vote
0
answers
52
views
0
answers
Scanpy vs DeSeq for single cell RNASeq DE gene analysis
... What are the advantages of either in this situation? Scanpy says it is for single cell DE analysis but if I am understandign correctly single cell RNASeq is just the same as any other normal bulk RNASeq but either on a single cell or specific subpopulation of cells? ...
rna-seq written 1 day ago by robert.murphy10
0
votes
0
answers
60
views
0
answers
Comment: C: How to convert gff to gbk format. I have the assembled fasta also
... Ah opps I though you were refering to the Augustus perl script `gff2gbSmallDNA.pl` from [here][1]. I will try the script you just linked. [1]: https://github.com/Gaius-Augustus/Augustus/blob/master/scripts/gff2gbSmallDNA.pl ...
written 9 days ago by robert.murphy10
0
votes
0
answers
60
views
0
answers
Comment: C: How to convert gff to gbk format. I have the assembled fasta also
... I am trying the script now but am stuck at what seems to be a requierd option called `max-size-of-gene-flanking-DNA`. I am not really sure what it is meant to be. ...
written 9 days ago by robert.murphy10
0
votes
0
answers
60
views
0
answers
Comment: C: How to convert gff to gbk format. I have the assembled fasta also
... I did and have seen this thread but the script the person mentions to use is not designed for standalone and has no guidance of how to operate it as such so I don't know how to use it. Plus with the thread being 9 and a half years old I thought it might be good to get an update of any better methods ...
written 9 days ago by robert.murphy10
0
votes
0
answers
60
views
0
answers
How to convert gff to gbk format. I have the assembled fasta also
... I have annotated a fungal genome with Augustus which outputs a GFF file fomat. I need the now run this genome through some downstreams tools that need GBK input as they for biosynthetic gene clusters within the sequence. How can I convert this GFF file to GBK? ...
genome written 9 days ago by robert.murphy10
0
votes
1
answer
80
views
1
answer
Convert gene sequence into protein sequence them HMM
... I want to take a gene sequence and identify if a metagenomic dataset posess this gene. I figured the best way to do this would be converting the gene sequence into a protein sequence and then into a HMM and using hmmsearch to look in the metagenomeic dataset. Firstly, is this a good approach? Sec ...
genome alignment written 15 days ago by robert.murphy10 • updated 15 days ago by Fatima350
0
votes
1
answer
85
views
1
answers
Comment: C: Cross referencing biosynthetic gene clusters in metagenome, best way to do this?
... How would I go about making alignments a biosynthetic gene cluster and then make a HMM ? Or if you mean of only specific genes inside the BGC how sould I pick genes to use and then again I I am unsure what you mean by make alignments. ...
written 15 days ago by robert.murphy10
0
votes
1
answer
131
views
1
answers
Comment: C: Can I use deseq on non transcriptome data?
... the normalisation was just to controll for different sequence depths as not all sequences came from the same run. Multiplying by 100 should not be viewed as a form of normalisation should it? it is just moving the space the counts occupy up a couple of factors? ...
written 24 days ago by robert.murphy10
1
vote
1
answer
131
views
1
answers
Comment: C: Can I use deseq on non transcriptome data?
... The abundances were calculated by taking all scaffolds in a bin and looking at their abundance in a sample. I have been given this abundace matrix so not 100% sure, but it was controlled for against a normalized depth so I think this is where the no integers come from I have just multiplied the whol ...
written 24 days ago by robert.murphy10

Latest awards to robert.murphy

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 771 users visited in the last hour