User: st.ph.n
st.ph.n • 2.4k
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Posts by st.ph.n
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... You can use the [Trinity][1] pipeline to align your SE/PE reads back to the transcriptome you assembled, which used Bowtie for alignment. The subsequent BAM files will be used to quantify abundance estimates.
[1]: https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Transcript-Quantifica ...
written 12 weeks ago by
st.ph.n • 2.4k
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... You can make any fasta into a blast database with `makeblastdb` ...
written 6 months ago by
st.ph.n • 2.4k
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824
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Comment:
C: tab to fasta file conversion
... *Try something*-there are multiple solutions. If you get stuck, post your efforts and errors. ...
written 6 months ago by
st.ph.n • 2.4k
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... > Since i am new to perl. Can anybody help me out with that?
If you post what you've tried, someone knowledgeable in Perl (if you *need* to use Perl) can help you figure out what might be wrong with your code. ...
written 6 months ago by
st.ph.n • 2.4k
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... yes, i'm still writing 2.7 syntax. ...
written 6 months ago by
st.ph.n • 2.4k
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... the `for` statement should be on a new line from the import statement. Looks like it must not have copied/pasted correctly. I commented out the actually renaming part, so you could test first and review the lines that are printed. ...
written 6 months ago by
st.ph.n • 2.4k
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566
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... Quick python solution.
#!/usr/bin/env python
import os, glob
for file in glob.glob("*.fastq.gz"):
# test with print statement
print file, '\t', file.split('_')[0] + '_' + file.split('_')[3] + '_.fastq.gz'
# uncomment to rename
# os.rename(file, file.split('_') ...
written 6 months ago by
st.ph.n • 2.4k
2
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4
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443
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4
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Answer:
A: headers from multifasta files
... for file in *.fasta; do grep -e '>' | cut -f 2 -d '>' > "`basename .fasta`.headers.txt"; done
Will take each file with `.fasta` extension in your `cwd` and `grep` for the headers, and cut the headers and take everything after the '>' and place them into a file named with the prefix ...
written 8 months ago by
st.ph.n • 2.4k
1
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436
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... Is this an assignment? Why not just use BLAST, and make on of your FASTA files the db? ...
written 8 months ago by
st.ph.n • 2.4k
2
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267
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... look into wrapping your command in `nohup` and `&` ...
written 8 months ago by
st.ph.n • 2.4k
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For A: single line fasta to mult line fasta
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For Upper Triangular Matrix From Array --Python
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For A: Using Trinity with case/control data
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For A: perl script for concatenating (multiple fasta sequences in a single file), creat
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