User: st.ph.n

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st.ph.n2.5k
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Philadelphia, PA
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Posts by st.ph.n

<prev • 562 results • page 1 of 57 • next >
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Comment: C: Biopython PRANK Alignment
... You have the command, but did you run it? Add another line with `prank_cline()` ...
written 12 months ago by st.ph.n2.5k
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Comment: C: Using trimmomatic on multiple single-end read files
... 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 14 months ago by st.ph.n2.5k
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Comment: C: Plotting Bar charts in R
... Do you have to use R? ...
written 15 months ago by st.ph.n2.5k
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Answer: A: Writing a bash loop to convert sams to bams
... for file in *.sam; do samtools view -S -b $file > "`basename $file .sam`.bam" done ...
written 15 months ago by st.ph.n2.5k
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Comment: C: Trouble with BLAST using Biopython
... Can you post more snippets of your script? ...
written 15 months ago by st.ph.n2.5k
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Answer: A: Split comma seperated list of GO terms into multiple rows and maintain gene iden
... #!/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 15 months ago by st.ph.n2.5k
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Comment: C: Mapping both PE reads and Single-end reads into transcriptome
... 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 21 months ago by st.ph.n2.5k
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Comment: C: BioPython local blast different results than blast+ local blast
... You can make any fasta into a blast database with `makeblastdb` ...
written 2.1 years ago by st.ph.n2.5k
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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 2.1 years ago by st.ph.n2.5k
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Comment: C: changing the position of a column from a file to another in perl
... > 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 2.1 years ago by st.ph.n2.5k

Latest awards to st.ph.n

Commentator 8 months ago, created a comment with at least 3 up-votes. For C: Removing a chromosome from a fasta file
Good Answer 10 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
Epic Question 10 months ago, created a question with more than 10,000 views. For Upper Triangular Matrix From Array --Python
Great Question 11 months ago, created a question with more than 5,000 views. For edirect: Entrez Unix Command line
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Simple amino acid polymorphism count
Epic Question 14 months ago, created a question with more than 10,000 views. For Upper Triangular Matrix From Array --Python
Popular Question 15 months ago, created a question with more than 1,000 views. For Python - Joining Overlapping DNA sequences
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Simple amino acid polymorphism count
Great Question 18 months ago, created a question with more than 5,000 views. For Upper Triangular Matrix From Array --Python
Popular Question 19 months ago, created a question with more than 1,000 views. For Python - Joining Overlapping DNA sequences
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Great Question 22 months ago, created a question with more than 5,000 views. For Upper Triangular Matrix From Array --Python
Popular Question 22 months ago, created a question with more than 1,000 views. For Python - Joining Overlapping DNA sequences
Popular Question 23 months ago, created a question with more than 1,000 views. For Python - Joining Overlapping DNA sequences
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Python - Joining Overlapping DNA sequences
Scholar 2.1 years ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 2.3 years ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Scholar 2.5 years ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Good Answer 2.5 years 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
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 2.6 years ago, created an answer that has been accepted. For A: Using Trinity with case/control data

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