User: st.ph.n

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st.ph.n2.4k
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Posts by st.ph.n

<prev • 556 results • page 1 of 56 • next >
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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 12 weeks ago by st.ph.n2.4k
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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 6 months ago by st.ph.n2.4k
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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 6 months ago by st.ph.n2.4k
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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 6 months ago by st.ph.n2.4k
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Comment: C: Batch rename *fastq.gz files using regular expression
... yes, i'm still writing 2.7 syntax. ...
written 6 months ago by st.ph.n2.4k
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Comment: C: Batch rename *fastq.gz files using regular expression
... the `for` statement should be on a new line from the import statement. Looks like it must not have copied/pasted correctly. I commented out the actually renaming part, so you could test first and review the lines that are printed. ...
written 6 months ago by st.ph.n2.4k
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Answer: A: Batch rename *fastq.gz files using regular expression
... Quick python solution. #!/usr/bin/env python import os, glob for file in glob.glob("*.fastq.gz"): # test with print statement print file, '\t', file.split('_')[0] + '_' + file.split('_')[3] + '_.fastq.gz' # uncomment to rename # os.rename(file, file.split('_') ...
written 6 months ago by st.ph.n2.4k
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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 8 months ago by st.ph.n2.4k
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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 8 months ago by st.ph.n2.4k
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Comment: C: downloading 1000 genomes project bam files in the background
... look into wrapping your command in `nohup` and `&` ...
written 8 months ago by st.ph.n2.4k

Latest awards to st.ph.n

Popular Question 4 days ago, created a question with more than 1,000 views. For Python - Joining Overlapping DNA sequences
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Great Question 3 months ago, created a question with more than 5,000 views. For Upper Triangular Matrix From Array --Python
Popular Question 4 months ago, created a question with more than 1,000 views. For Python - Joining Overlapping DNA sequences
Popular Question 5 months ago, created a question with more than 1,000 views. For Python - Joining Overlapping DNA sequences
Popular Question 6 months ago, created a question with more than 1,000 views. For Python - Joining Overlapping DNA sequences
Scholar 6 months ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Teacher 6 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 11 months ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Good Answer 11 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
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
Great Question 14 months ago, created a question with more than 5,000 views. For Finding Min Value In List Of Lists -- Python -- Without Numpy
Great Question 15 months ago, created a question with more than 5,000 views. For Upper Triangular Matrix From Array --Python
Scholar 15 months ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Student 15 months ago, asked a question with at least 3 up-votes. For Truncated SAM file - odd characters
Great Question 15 months ago, created a question with more than 5,000 views. For Python- Find ORF in sequence, compound return statement
Scholar 15 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: conditional replacing rows with 9
Scholar 15 months ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 16 months ago, created an answer that has been accepted. For A: Using Trinity with case/control data

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