User: st.ph.n

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st.ph.n2.2k
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Philadelphia, PA
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Posts by st.ph.n

<prev • 549 results • page 1 of 55 • next >
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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 7 days ago by st.ph.n2.2k
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Comment: C: Finding pairwise alignment between two multifasta files for similarity search
... Is this an assignment? Why not just use BLAST, and make on of your FASTA files the db? ...
written 26 days ago by st.ph.n2.2k
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Comment: C: downloading 1000 genomes project bam files in the background
... look into wrapping your command in `nohup` and `&` ...
written 27 days ago by st.ph.n2.2k
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Comment: C: Translating Plant DNA to protein
... BLASTX will only align DNA to protein. If you need to translate sequences, there are command line tools to do so, as well as modules for different programming languages, such as Biopython. Are your sequences in frame? ...
written 28 days ago by st.ph.n2.2k
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Comment: C: help in converting a table
... I'm more use to 2.X syntax so I wasn't aware. Thanks. ...
written 6 weeks ago by st.ph.n2.2k
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Comment: C: Removing a chromosome from a fasta file
... I would also double check that the sequence is the same. ...
written 6 weeks ago by st.ph.n2.2k
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Comment: C: help in converting a table
... Sometimes new line characters aren't interpreted properly, depending on how you're opening your file, e.g. notepad. Trying using the command-line, `less output.txt`, or open in Excel if it is not too large. ...
written 6 weeks ago by st.ph.n2.2k
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Comment: C: help in converting a table
... How many times does `hsa-mir-4649` appear in your input file? This should equal (+1) the number of columns in the output for that gene id. grep -e 'hsa-mir-4649' | wc -l How many genes in your input file? How many lines in your output file? These should be identical. cut -f 1 input.txt | ...
written 6 weeks ago by st.ph.n2.2k
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Answer: A: help in converting a table
... Here's a quick python solution. I'm assuming your table is tab-delimited, and it will output tab-delimited. #!/usr/bin/env python import sys from collections import defaultdict with open(sys.argv[1], 'r') as f: genes = defaultdict(list) for line in f: genes[lin ...
written 6 weeks ago by st.ph.n2.2k
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Comment: C: changing header name in fasta file
... Try something. If you get stuck, or get an error - post the output and error message. ...
written 9 weeks ago by st.ph.n2.2k

Latest awards to st.ph.n

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

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