User: st.ph.n

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st.ph.n2.5k
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Posts by st.ph.n

<prev • 561 results • page 1 of 57 • next >
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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 7 weeks ago by st.ph.n2.5k
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Comment: C: Plotting Bar charts in R
... Do you have to use R? ...
written 9 weeks 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 12 weeks 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 12 weeks 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 3 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 8 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 12 months 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 12 months 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 12 months ago by st.ph.n2.5k
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Comment: C: Batch rename *fastq.gz files using regular expression
... yes, i'm still writing 2.7 syntax. ...
written 12 months ago by st.ph.n2.5k

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
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
Great Question 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 12 months ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Scholar 15 months ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Scholar 17 months ago, created an answer that has been accepted. For A: Using Trinity with case/control data
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, created a question with more than 5,000 views. For Finding Min Value In List Of Lists -- Python -- Without Numpy
Great Question 20 months ago, created a question with more than 5,000 views. 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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