User: ole.tange

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ole.tange3.7k
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Posts by ole.tange

<prev • 92 results • page 1 of 10 • next >
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Comment: C: How to rename multiple fastq files
... parallel --dry-run mv {} '{=s/GEN\d+_N_(\w+)_lib\d+_\d+_(\d+_R\d)/$1_$2/=}' ::: *.fastq ...
written 6 weeks ago by ole.tange3.7k
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Answer: A: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
... **EXAMPLE: Call program with FASTA sequence** FASTA files have the format: ...
written 4 months ago by ole.tange3.7k
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Answer: A: Calculating Shannon entropy for RNA sequences in multi-fasta using rnaentropy
... With GNU Parallel (https://www.biostars.org/p/63816/) you would do: cat in.fasta | parallel --pipe -N1 --recstart '>' --rrs 'read a; echo Doing "$a"; ./RNAentropy -s $(tr -d "\n")' From [GNU Parallel Tutorial: Informational](https://www.gnu.org/software/parallel/parallel_tutoria ...
written 5 months ago by ole.tange3.7k • updated 5 months ago by zx87549.1k
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Answer: A: bwa mem: fail to locate the index files
... GNU Parallel does not run its jobs in the same shell session as it is started. That means that non-exported variables and non-exported functions cannot be seen. However, `env_parallel` can make a copy of the environment in the current session and pass that to GNU Parallel. By using `env_parallel -- ...
written 8 months ago by ole.tange3.7k
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Answer: A: using GNU parallel for bwa mem and samtools
... It makes it easier to read and to test if you create a function and call that. You can then test your function on a single file set before handing it to GNU Parallel: bwatosam() { id="$1" bwa mem -t 10 -M -R "@RG\tID:{}\tSM:{}\tPL:ILLUMINA\tLB:{}" hg1kv37.fa "$id"_R1.fq.gz "$i ...
written 8 months ago by ole.tange3.7k
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Comment: C: How to extract filename and change text in the same file
... It is covered in GNU Parallel 2018 chapter 5 (Online https://doi.org/10.5281/zenodo.1146014, printed www.lulu.com/shop/ole-tange/gnu-parallel-2018/paperback/product-23558902.html) ...
written 13 months ago by ole.tange3.7k
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Comment: C: How to extract filename and change text in the same file
... Fix: `vc$f` -> `vcf\$`. Also try: `parallel --plus 'sed -i "s|Sample1$|{%.new.vcf}|"' {} ::: *.new.vcf` ...
written 13 months ago by ole.tange3.7k
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Answer: A: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
... GNU Parallel now has a cheat sheet: https://www.gnu.org/software/parallel/parallel_cheat.pdf ...
written 13 months ago by ole.tange3.7k
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Comment: C: How to speed up trimming using trim galorer
... Shorter: parallel --plus 'trim_galore --paired {...}.R1.fq.gz {...}.R2.fq.gz' ::: *R1.fq.gz ...
written 14 months ago by ole.tange3.7k
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Comment: C: How to run SNPEff jar for a batch of VCF files using GNU parallel tool?
... If you add an example of how you do it without GNU Parallel, then you may have more luck getting a usable answer. ...
written 15 months ago by ole.tange3.7k

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Appreciated 4 months ago, created a post with more than 5 votes. For A: Gnu Parallel Quoting With Awk
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Gnu Parallel Quoting With Awk
Appreciated 5 months ago, created a post with more than 5 votes. For A: Gnu Parallel Quoting With Awk
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: What is the correct way to use GNU parallel with Primer3?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: What is the correct way to use GNU parallel with Primer3?
Scholar 8 months ago, created an answer that has been accepted. For A: What is the correct way to use GNU parallel with Primer3?
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: Gnu Parallel Quoting With Awk
Appreciated 10 months ago, created a post with more than 5 votes. For A: Gnu Parallel Quoting With Awk
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: What is the correct way to use GNU parallel with Primer3?
Appreciated 17 months ago, created a post with more than 5 votes. For A: Gnu Parallel Quoting With Awk
Appreciated 21 months ago, created a post with more than 5 votes. For A: Gnu Parallel Quoting With Awk
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: What is the correct way to use GNU parallel with Primer3?
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: What is the correct way to use GNU parallel with Primer3?
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Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: What is the correct way to use GNU parallel with Primer3?
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: What is the correct way to use GNU parallel with Primer3?
Scholar 4.2 years ago, created an answer that has been accepted. For A: What is the correct way to use GNU parallel with Primer3?
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Got Multiple Cpus? Activate Them With Gnu Parallel
Good Answer 5.0 years ago, created an answer that was upvoted at least 5 times. For A: Piping With Samtools, Bwa And Bedtools
Teacher 5.0 years ago, created an answer with at least 3 up-votes. For A: Gnu Parallel Quoting With Awk
Scholar 5.0 years ago, created an answer that has been accepted. For A: What is the correct way to use GNU parallel with Primer3?
Appreciated 5.2 years ago, created a post with more than 5 votes. For Got Multiple Cpus? Activate Them With Gnu Parallel
Teacher 5.6 years ago, created an answer with at least 3 up-votes. For A: Piping With Samtools, Bwa And Bedtools
Popular Question 5.8 years ago, created a question with more than 1,000 views. For Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them

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