User: st.ph.n
st.ph.n • 2.5k
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- Philadelphia, PA
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Posts by st.ph.n
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... List your files in a text file. If they are all in a folder called raw, and you want to run from there, the filenames in the SE_files.txt would be raw/*prefix*.fastq.gz. The point is you're putting the command in a bash script, and then looping through each line (file) in the text one at a time.
S ...
written 7 weeks ago by
st.ph.n • 2.5k
0
votes
1
answer
146
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1
answers
Comment:
C: Plotting Bar charts in R
... Do you have to use R? ...
written 9 weeks ago by
st.ph.n • 2.5k
1
vote
1
answer
168
views
1
answers
... for file in *.sam; do
samtools view -S -b $file > "`basename $file .sam`.bam"
done ...
written 12 weeks ago by
st.ph.n • 2.5k
0
votes
1
answer
206
views
1
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... Can you post more snippets of your script? ...
written 12 weeks ago by
st.ph.n • 2.5k
1
vote
3
answers
182
views
3
answers
... #!/usr/bin/env python
import sys
with open(sys.argv[1], 'r') as f:
for line in f:
for n in range(len(line.strip().split('\t')[1].split(','))):
print line.strip().split('\t')[0] + 't' + line.strip().split('\t')[1].split(',')[n]
Save as `go_tab. ...
written 3 months ago by
st.ph.n • 2.5k
0
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0
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304
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answers
... 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 8 months ago by
st.ph.n • 2.5k
0
votes
0
answers
431
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0
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... You can make any fasta into a blast database with `makeblastdb` ...
written 12 months ago by
st.ph.n • 2.5k
0
votes
2
answers
1.5k
views
2
answers
Comment:
C: tab to fasta file conversion
... *Try something*-there are multiple solutions. If you get stuck, post your efforts and errors. ...
written 12 months ago by
st.ph.n • 2.5k
1
vote
0
answers
288
views
0
answers
... > 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 12 months ago by
st.ph.n • 2.5k
1
vote
3
answers
804
views
3
answers
... yes, i'm still writing 2.7 syntax. ...
written 12 months ago by
st.ph.n • 2.5k
Latest awards to st.ph.n
Teacher
27 days ago,
created an answer with at least 3 up-votes.
For A: Simple amino acid polymorphism count
Appreciated
6 weeks ago,
created a post with more than 5 votes.
For A: perl script for concatenating (multiple fasta sequences in a single file), creat
Epic Question
7 weeks ago,
created a question with more than 10,000 views.
For Upper Triangular Matrix From Array --Python
Popular Question
3 months ago,
created a question with more than 1,000 views.
For Python - Joining Overlapping DNA sequences
Teacher
4 months ago,
created an answer with at least 3 up-votes.
For A: Simple amino acid polymorphism count
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5 months ago,
created a question with more than 5,000 views.
For Upper Triangular Matrix From Array --Python
Popular Question
6 months ago,
created a question with more than 1,000 views.
For Python - Joining Overlapping DNA sequences
Teacher
8 months ago,
created an answer with at least 3 up-votes.
For A: single line fasta to mult line fasta
Great Question
9 months ago,
created a question with more than 5,000 views.
For Upper Triangular Matrix From Array --Python
Popular Question
10 months ago,
created a question with more than 1,000 views.
For Python - Joining Overlapping DNA sequences
Popular Question
11 months ago,
created a question with more than 1,000 views.
For Python - Joining Overlapping DNA sequences
Popular Question
12 months ago,
created a question with more than 1,000 views.
For Python - Joining Overlapping DNA sequences
Teacher
12 months ago,
created an answer with at least 3 up-votes.
For A: single line fasta to mult line fasta
Scholar
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For A: Using Trinity with case/control data
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15 months ago,
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For A: Using Trinity with case/control data
Scholar
17 months ago,
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For A: Using Trinity with case/control data
Appreciated
17 months ago,
created a post with more than 5 votes.
For A: perl script for concatenating (multiple fasta sequences in a single file), creat
Good Answer
17 months ago,
created an answer that was upvoted at least 5 times.
For A: perl script for concatenating (multiple fasta sequences in a single file), creat
Scholar
18 months ago,
created an answer that has been accepted.
For A: Using Trinity with case/control data
Teacher
18 months ago,
created an answer with at least 3 up-votes.
For A: single line fasta to mult line fasta
Great Question
20 months ago,
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For Finding Min Value In List Of Lists -- Python -- Without Numpy
Great Question
20 months ago,
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For Upper Triangular Matrix From Array --Python
Teacher
21 months ago,
created an answer with at least 3 up-votes.
For A: single line fasta to mult line fasta
Scholar
21 months ago,
created an answer that has been accepted.
For A: Using Trinity with case/control data
Student
21 months ago,
asked a question with at least 3 up-votes.
For Truncated SAM file - odd characters
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