User: Daniel
Daniel • 3.6k
- Reputation:
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- Location:
- Cardiff University
- Last seen:
- 3 days, 22 hours ago
- Joined:
- 7 years, 5 months ago
- Email:
- d*****************@googlemail.com
Posts by Daniel
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1
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3
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185
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3
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... The $n parameters are the columns when you divide the file up by what is inside the -F'[ ]' box, so if you split the line every time you saw a space, asterix, colon, or period then you'd want the 5th, 6th, 8th and 13th columns to be printed. ...
written 7 weeks ago by
Daniel • 3.6k
0
votes
3
answers
185
views
3
answers
... Huh, I was certain that bed format was colon and hyphen but the internet doesn't support that... Maybe I'm going mad. Ok, updating.
Edit: I was thinking of UCSC browser formatting apparently. ...
written 7 weeks ago by
Daniel • 3.6k
4
votes
3
answers
185
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3
answers
... My approach is lazier... Just split on the punctuation, pull out the columns you want, and separate by "\t".
awk -F'[ *:.]' -v OFS="\t" '{print "chr"$5,$6,$8,$13}' tmp.txt
# Output
chr2L 22300300 22304444 invader2
...
written 7 weeks ago by
Daniel • 3.6k
0
votes
0
answers
155
views
0
answers
... There are lots of questions regarding this, and I have asked them myself over the years, but I've recently found this tool which is great and I thought I'd put a standard example. This might not be the best way of parsing the outputs in R, but as a tool it generates all the right data!
library( ...
written 10 weeks ago by
Daniel • 3.6k
0
votes
2
answers
341
views
2
answers
Comment:
C: convert illumina to fastq Sanger
... Please explain what you are trying to achieve and why, so that we can help you, as this request is confusing. Do you have a bcl file? ...
written 8 months ago by
Daniel • 3.6k
2
votes
2
answers
2.0k
views
2
answers
... There are lots of jokes above, but the honest answer is that you do not want to do this. Once you have converted the file it would be so massive that it would impossible to open and use in excel before any other problems. Further, this is not an appropriate way to read the data, and 99.9% of the tim ...
written 9 months ago by
Daniel • 3.6k
2
votes
6
answers
1.3k
views
6
answers
... Seconding the 'finding my own posts' point, only yesterday I was trying to find an old answer of mine to put to a duplicate question and gave up after 5 mins of searching and scrolling because I couldn't find it. ...
written 12 months ago by
Daniel • 3.6k
4
votes
6
answers
1.3k
views
6
answers
... I think the difficulty searching adds to the repeated low quality questions. ...
written 12 months ago by
Daniel • 3.6k
3
votes
6
answers
1.3k
views
6
answers
... I think that could be solved quite easily with (1 ) a more restricted set of tags for questions to stop fragmenting, and (2) allowing them to be community-suggested so that new users don't have to be blamed for misattributing a question (this works quite well for games on steam) i.e.
> **Based o ...
written 12 months ago by
Daniel • 3.6k
1
vote
3
answers
693
views
3
answers
Comment:
C: else condition in awk
... If it's not working don't click 'accept' and tell us what the error is. ...
written 15 months ago by
Daniel • 3.6k
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For RNAseq comparisons (tophat->HTSeq->edgeR) return only a few sig diffs, and all snRNA. Pos. bias? Further options?
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For A: Correcting sequence reads based on ORF disruption from reference sequence.
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For A: Convert Fas/Qual Into Fastq?
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For Is there a more optimal SAM orientation parsing method?
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For Parsing Genbank Format In Bioperl.
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For A: Conferences On Bioinformatics
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For C: Why Didn'T Biostar Join Stack Exchange?
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12 months ago,
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13 months ago,
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For A: Conferences On Bioinformatics
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For Travel and accommodation bursaries for workshops on Gene expression analysis, Metabolomics, RAD analysis or Population genomics in Environmental ‘Omics
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16 months ago,
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For A: Correcting sequence reads based on ORF disruption from reference sequence.
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For Rdp, Greengenes And Arb-Silva. Are There Any Advantages Of One Over The Other?
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18 months ago,
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