User: Fatima
Fatima • 930
- Reputation:
- 930
- Status:
- Trusted
- Location:
- United states
- Website:
- https://homes.luddy.in...
- Twitter:
- fsharifi4
- Scholar ID:
- Google Scholar Page
- Last seen:
- 17 hours ago
- Joined:
- 4 years, 3 months ago
- Email:
- f************@gmail.com
myRT (RT Identification/Classification)
Fun4me (Functional Annotation for Metagenomes)
myDGR (Identification of DGR systems)
FragGeneScan (Gene Predictor)
PROPER (Performance visualization in MATLAB)
Posts by Fatima
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... Please try uploading your file to ITOL and see if you get a different result (it's easy to use):
https://itol.embl.de/upload.cgi
Could you tell me the accession number of the ancestor node? ...
written 3 days ago by
Fatima • 930
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... Hi! Have you tried these packages? You may want to give them a try.
https://cran.r-project.org/web/packages/castor/index.html
https://guangchuangyu.github.io/software/treeio/ ...
written 5 days ago by
Fatima • 930
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... Can you use MetaCyc instead?
https://biodatamining.biomedcentral.com/articles/10.1186/s13040-018-0166-8
See data/pathways.info
https://sourceforge.net/p/fun4me/code/ci/master/tree/
...
written 10 days ago by
Fatima • 930
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... Have you tried changing the headers of the files (go_id to go), and then get the list of attributes?
The link to the post in your original question doesn't work. Are you referring to this post?
https://www.biostars.org/p/354675/
Another good resource:
https://www.stat.berkeley.edu/~sandrine/ ...
written 23 days ago by
Fatima • 930
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... I think "filters" should match with attributes and headers of the data. So, if you're using "go" as filters, the header and attribute should also be "go" instead of "go_id", or you can use filters="go_id" to match. ...
written 23 days ago by
Fatima • 930
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... Hi, you can use `metaCyc`. Check `Fun4me` for more information.
https://link.springer.com/protocol/10.1007/978-1-4939-7015-5_3
https://sourceforge.net/projects/fun4me/ ...
written 27 days ago by
Fatima • 930
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... If your sequences are one and only one line you can use:
grep -A 1 ";partial=00;" file > file1
grep -A 1 -E ";partial=01;|;partial=10;|;partial=11;" file > file2
If your sequences occupy more that one line, you can use this command to convert your sequences:
awk '/^>/ { ...
written 27 days ago by
Fatima • 930
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148
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... Are the headers exactly identical?
grep "16S_rRNA" filename > headers
#This is not very efficient but should do the work
cat headers | sort | uniq | while read line ; do grep -A 1 "${line}" filename >> output ; done ...
written 28 days ago by
Fatima • 930
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... You can use cd-hit with cutoff value of 1 (-c 1), it will remove the redundant sequences, but will also remove them if their header is different (as long as sequences are identical). So, for example when you have three identical sequences, the output file will only contain one of them ( the represen ...
written 29 days ago by
Fatima • 930
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... If each sequence is **one and only one line:**
grep -A 1 "16S_rRNA:" filename
Should do the trick! ...
written 29 days ago by
Fatima • 930
Latest awards to Fatima
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4 months ago,
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For A: bash script for RNA seq analysis
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For Samtools depth input
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For Samtools depth input
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For A: bash script for RNA seq analysis
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12 months ago,
created an answer that has been accepted.
For A: bash script for RNA seq analysis
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13 months ago,
created an answer that has been accepted.
For A: bash script for RNA seq analysis
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For Parsing gff files using python and awk
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For concatenating different columns of different files bash script
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3.4 years ago,
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