User: cpad0112
cpad0112 • 8.9k
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Posts by cpad0112
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Comment:
C: MEGAN Group Comparison
... For future reference:
http://megan.informatik.uni-tuebingen.de/t/how-to-compare-groups/415
...
written 2 hours ago by
cpad0112 • 8.9k
1
vote
2
answers
83
views
2
answers
... For pathways, KEGG and for functions in a cell, try GO:MF ...
written 7 hours ago by
cpad0112 • 8.9k
1
vote
1
answer
63
views
1
answers
... Try ensembl variation api ...
written 14 hours ago by
cpad0112 • 8.9k
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0
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79
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Comment:
C: GRCh37.p13 download at NCBI FTP?
... Download GRCh37.p13 single fasta file from Gencode:
ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/GRCh37.p13.genome.fa.gz
or from here with index as well: http://bioinfo.hpc.cam.ac.uk/downloads/datasets/fasta/grch37/
...
written 1 day ago by
cpad0112 • 8.9k
0
votes
1
answer
150
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1
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Comment:
C: Parsing header of FASTA File
... Assuming that fasta is linearized (i.e sequence is in single line, after header):
sed -n '/>/p' test.fa | grep -vw chromosome | grep --no-group-separator -f - -A 1 test.fa
should give you all the fasta sequences with no chromosome in header.
sed -n '/>/p' test.fa | grep -w chromoso ...
written 1 day ago by
cpad0112 • 8.9k
3
votes
1
answer
112
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1
answers
... > The output peptide sequence is always in the standard one-letter
> IUPAC code.
http://structure.usc.edu/emboss/transeq.html
and try this:
$ echo atgtttcaggacccacaggagtaa | showseq -filter -threeletter y -format 4
10 20
----:----|----:----|----
...
written 1 day ago by
cpad0112 • 8.9k
2
votes
1
answer
60
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1
answers
... `scale = "row"` and `scale = "none"` in conflict in your function, you defined them twice. ...
1
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4
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400
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4
answers
... a little late to the party:
$ sed '/>/ s/^.*__\(\w\+\)__.*/>\1/g' file.fa
or
$ sed '/>/ s/^\(\W\).*__\(\w\+\)__.*/\1\2/g' file.fa
>778568
GCTGGCGACGGATCTAGGCTCAGCGCAGAAGCAACTGAGAGTCGGCGATGAGCAGCCGGA
GCTGGCGACGGATCTAGGCTCAGCGCAGAAGCAA
>778569
GCT ...
written 2 days ago by
cpad0112 • 8.9k
0
votes
3
answers
105
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3
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Comment:
C: how to change fasta headers?
... try this: https://www.biostars.org/u/21479/
$ sed '/>/ s/^\(>\w\+.\w\).*/\1/g' file.fa
or
$ sed '/>/ s/^\(.*\.\w\).*/\1/g' file.fa
>WP_000580188.1
MIGQQRNILATLGIDVWIPRTQVCQKNNAHTLWRDQVVEPHESITVPTIDVPAFEQKNTQPQVLEIPKVVEEPPIVVAEVSQPEILVEKPKVIEQETITPFELQAYCLEKCVIFVDVTAL ...
written 2 days ago by
cpad0112 • 8.9k
1
vote
3
answers
105
views
3
answers
Answer:
A: how to change fasta headers?
... $ sed '/>/ s/.*_\([A-Z]\{2\}_[0-9]\+.[0-9]\).*/>\1/g' test.fa
or
$ sed '/>/ s/.*=\([A-Z]\+_[0-9]\+.[0-9]\).*/>\1/g' test.fa
>WP_000637306.1
MIVSNNFAVPYYLNVRKEKGMTAYYWATHQSQLALFDSYELAYRFYFPSRHILIRSEIKAFAQ
>WP_000572517.1
MIEQIQKRSLVDEVIHVIRQNIKNDIWKVDEKI ...
written 2 days ago by
cpad0112 • 8.9k
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For C: Problem installing Rgraphviz in R
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For C: can someone read this result to me
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