User: rob234king
rob234king • 560
- Reputation:
- 560
- Status:
- Trusted
- Location:
- UK/Harpenden/Rothamsted Research
- Website:
- http://elvis.misc.cran...
- Last seen:
- 2 days, 15 hours ago
- Joined:
- 5 years, 6 months ago
- Email:
- r*********@gmail.com
Cranfield University MSc Applied Bioinformatics, Queen Mary University of London PhD Cancer Radiopharmaceuticals. Employed at Rothamsted Research.
Posts by rob234king
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Answer:
A: for extension of gene family
... orthomcl all the proteins and see if those you know have additional included in orthomcl. google orthomcl and can use web version or download ...
written 10 weeks ago by
rob234king • 560
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... I will give CAMSA a go which looks like might do what I want and update but any other ideas, please let me know
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1919-y
...
written 3 months ago by
rob234king • 560
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Comment:
C: merging 10X genomics assemblies
... from the 10X stats which don't match a perl script I have in terms of size of genome etc, but ignoring that, the assembly is better in terms of assembling more but consequently the N50 goes down. However when go beyond numbers and look at genes then there is some variation in terms of scaffolding wh ...
written 3 months ago by
rob234king • 560
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... I have different 10X genomics data assemblies using different subsets of reads with supernova 2.01. We have what should be the best assembly with ideal x42 but when I look at some genes, one of the subset read assemblies will have the missing contig placed for one gene that was missed in the best as ...
written 3 months ago by
rob234king • 560
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Comment:
C: script for task or AWK
... I can do this last bit in excel. Thanks this saved me so much time trying to get a perl script to dot he same! ...
written 4 months ago by
rob234king • 560
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Comment:
C: script for task or AWK
... I would only need the lead chromosome for each so below. Guess then for each sequence I could take the highest value in the end column some how.
seq000001 Fc06 35.948-51.086 72
seq000002 Fc09 13.078-39.857 34 ...
written 4 months ago by
rob234king • 560
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Comment:
C: script for task or AWK
... damn, that easy? I'll download datamash, will it also report how many markers there were, I made a change to what I was looking for above but already something to work with. thanks. ...
written 4 months ago by
rob234king • 560
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8 follow
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... I have tried to break a problem down to two files. I want to take the most common 2nd column value for each sequence (1st column) then have the range of column 3 for those values. Also count the number of markers so the number of Fc06 for seq000001. Any idea how to do this? I was hoping for somethin ...
written 4 months ago by
rob234king • 560
• updated
4 months ago by
dariober ♦ 9.6k
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... I have had errors getting falcon unzip to work on a pacbio assembly but believe I have got to an end by launching jobs manually. I had to change one of the scripts as -mum for nucmer was an option when should have been --mum and was causing an error (I did post on github about this).
What I think ...
written 5 months ago by
rob234king • 560
• updated
7 weeks ago by
alslonik • 30
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... I got the test data to run using the config file provided in tutorial. It looks like was successful. The raw data was fasta. I just tested with fastq data and ends with error. From ENA they quite often provide the data in fastq so using this tools looks like I can convert https://github.com/zyndagj ...
written 7 months ago by
rob234king • 560
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