User: st.ph.n

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st.ph.n1.9k
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Philadelphia, PA
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2 days, 13 hours ago
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Posts by st.ph.n

<prev • 507 results • page 1 of 51 • next >
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Answer: A: Find consensus sequence of several DNA sequences
... You can use [Biopython][1] to create a consensus sequence. #!/usr/bin/env python import sys from Bio import AlignIO from Bio.Align import AlignInfo alignment = AlignIO.read(sys.argv[1], 'fasta') summary_align = AlignInfo.SummaryInfo(alignment) summary_align.du ...
written 4 days ago by st.ph.n1.9k
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Comment: C: Trying to get a GREP of things...
... put this in bash script: #!/usr/bin/bash grep -e "$1" flyBaseGene.txt >> results.txt save as `grep_gene.sh`, then: cat Genes_of_interest.txt | xargs -n 1 bash grep_gene.sh ...
written 8 days ago by st.ph.n1.9k
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Comment: C: Trying to get a GREP of things...
... cat Genes_of_interest.txt | grep -e "$1" flyBaseGene.txt > results.txt ...
written 8 days ago by st.ph.n1.9k
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Comment: C: Help with Fastq-Tools Install
... You can install locally to your home folder. Check the `README`, or program manual for the software. If there's a `configure` script, typically one can use `--prefix` to provide the install path, prior to running `make install`. As is a university computer, check with someone first. If it is a lab s ...
written 10 days ago by st.ph.n1.9k
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Comment: C: Help with Fastq-Tools Install
... Is this your own computer? Looks like you don't have permissions to install globally. ...
written 10 days ago by st.ph.n1.9k
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Comment: C: Fail running blastdb and blastn on my own computer
... Post the commands exactly as you're running them. Alternatively, try your commands in the windows shell, and see if they work, you might be able to see the error, if there is one. Also, try '\' or '\\' instead of '/' in your path. ...
written 10 days ago by st.ph.n1.9k
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Comment: C: Fail running blastdb and blastn on my own computer
... C:/Program Files/NCBI/blastn-2.6.0+/bin/makeblastdb.exe-in Must be copy/paste error. There needs to be a space before `-in` ...
written 11 days ago by st.ph.n1.9k
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Comment: C: Fail running blastdb and blastn on my own computer
... Try without -`out` flag, makeblastdb will automake the necessary files with extensions to your ref_file. ...
written 14 days ago by st.ph.n1.9k
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Comment: C: Fail running blastdb and blastn on my own computer
... Ceck in the folder where `Ref_file` is ...
written 14 days ago by st.ph.n1.9k
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Comment: C: Fail running blastdb and blastn on my own computer
... What happens when you run it like this, and don't break up the code: import subprocess subprocess.call("C:/Program Files/NCBI/blastn-2.6.0+/bin/makeblastdb.exe -in " + Ref_file + " -dbtype nucl -parse_seqids -out Blastdatabase.out", shell=True) subprocess.call("C:/Program Fil ...
written 14 days ago by st.ph.n1.9k

Latest awards to st.ph.n

Great Question 22 days ago, created a question with more than 5,000 views. For Finding Min Value In List Of Lists -- Python -- Without Numpy
Great Question 4 weeks ago, created a question with more than 5,000 views. For Upper Triangular Matrix From Array --Python
Scholar 6 weeks ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Student 6 weeks ago, asked a question with at least 3 up-votes. For Truncated SAM file - odd characters
Great Question 6 weeks ago, created a question with more than 5,000 views. For Python- Find ORF in sequence, compound return statement
Scholar 7 weeks ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Scholar 8 weeks ago, created an answer that has been accepted. For A: conditional replacing rows with 9
Scholar 8 weeks ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Scholar 9 weeks ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 10 weeks ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 3 months ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Scholar 3 months ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Scholar 3 months ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Scholar 3 months ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Scholar 4 months ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Scholar 4 months ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Guru 4 months ago, received more than 100 upvotes.
Scholar 4 months ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Scholar 5 months ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Scholar 6 months ago, created an answer that has been accepted. For A: Using Trinity with case/control data

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