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User: rob234king

gravatar for rob234king
rob234king • 560
Reputation:
560
Status:
Trusted
Location:
UK/Harpenden/Rothamsted Research
Website:
http://elvis.misc.cran...
Last seen:
2 months ago
Joined:
5 years, 10 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

<prev • 160 results • page 1 of 16 • next >
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Comment: A: merging 10X genomics assemblies
... didn't try it in the end as got some long reads to do hybrid assembly anyway. surprised there were some snps in 10X assemblies that were mistakes too. ...
written 12 weeks ago by rob234king • 560
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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 6 months ago by rob234king • 560
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Answer: A: merging 10X genomics assemblies
... 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 7 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 7 months ago by rob234king • 560
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merging 10X genomics assemblies
... 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 ...
10x written 7 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 8 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 8 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 8 months ago by rob234king • 560
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script for task or AWK
... 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 ...
script awk written 8 months ago by rob234king • 560 • updated 8 months ago by dariober ♦ 9.9k
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falcon unzip output
... 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 ...
falcon pacbio written 9 months ago by rob234king • 560 • updated 5 months ago by alslonik • 70

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