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updated 2.9 years ago by
Michael R. Crusoe
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Recent Replies
Comment: Using outgroup in gene family dendograms
by
Mensur Dlakic
★
10k
> Wouldn't a gene that isn't an ABC superfamily member from some distant species suffice as an outgroup candidate here?
Most definitely no…
Comment: Testing independence between 5' and 3' terminal sequences in a DNA database
by
Istvan Albert
87k
with that definition I would suspect that all of your sequences are "dependent", I would expect every functional DNA/RNA region to capture …
Comment: Taxonomy assignment of viral RNA
by
biobiu
▴
120
Thanks!
As for the blast option- (1) so do you suggest to just blast the contig against a db of viral RNAs? and (2) is there a comprehensiv…
Comment: Finding how many times a nucleotide appear in the same position
by
cpad0112
15k
#!/usr/bin/env python3
sequences = ["GAGGTAAACTCTG", "TCCGTAAGTTTTC", "CAGGTTGGAACTC", "ACAGTCAGTTCAC", "TAGGTCATTACAG", "TAGG…
Comment: Testing independence between 5' and 3' terminal sequences in a DNA database
by
Anand Rao
▴
350
Thanks for your reply. Yes, I think I could have explained my problem much better, but rather than change my original post, I will add some…
Answer: Finding how many times a nucleotide appear in the same position
by
Dunois
▴
600
Here's a little `python` function you can work off of:
def count_quer_at_pos_in_seq(seqs, quer = "A"):
#Initialize a list…
Comment: Using outgroup in gene family dendograms
by
Rogerio Ribeiro
▴
50
Thank for the fast reponse. The ABC family is not the best example for this question indeed.
The objective of my work is to find genes resp…
Answer: Taxonomy assignment of viral RNA
by
Zhilong Jia
★
1.7k
1. Blast directly
2. [IDSeq][1], can get viral contigs and their annotation directly.
[IDSeq : An open-source cloud-based pipeline and…
Comment: Finding how many times a nucleotide appear in the same position
by
hugo.avila
▴
180
Hi, It is not a norm but it is a good practice to post an attempted resolution first and then other members try to correct it or suggest an…
Comment: What Do You Waste Your Time On
by
ponganta
▴
150
Aye to the rushed analyses and the last-minute documentation. Horrible, but somehow it happens all the time.
Answer: What Do You Waste Your Time On
by
ponganta
▴
150
Reinventing the wheel. Like, all the time. Why use clusterProfiler with an up-to-date GO-annotation, when you can just write your own clien…
Comment: RNAseq data analysis of pooled data
by
ponganta
▴
150
By "pooled" data, do you mean data from tissue-specific bulk-RNAseq?
Or did you pool single cell (SC) RNAseq-libraries?
Comment: RNAseq data analysis of pooled data
by
Dunois
▴
600
What exactly do you mean by "pooled" data?
Answer: RNAseq data analysis of pooled data
by
grant.hovhannisyan
★
2.1k
I made a tutorial last year for University students on this topic https://www.loom.com/share/a55c1dedb8e64e7cac47f6595b751de7. Let me know …
Comment: RNAseq data analysis of pooled data
by
luffy
•
0
@dunois Thank you for the tutorial, what are your thoughts for approach for pooled data? should i follow the documentation/the tutorial or …
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