User: ole.tange

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ole.tange3.4k
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Posts by ole.tange

<prev • 87 results • page 1 of 9 • next >
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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 11 days ago by ole.tange3.4k
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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 14 days ago by ole.tange3.4k
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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 16 days ago by ole.tange3.4k
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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 9 weeks ago by ole.tange3.4k
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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 3 months ago by ole.tange3.4k
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7 follow
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Tool: Book: GNU Parallel 2018 - for beginners and advanced users
... [GNU Parallel][1] is often used in bioinformatics. To make it easier to get started there is now a book. The book "GNU Parallel 2018" is available [in print][2] or [online][3]. If you have never used GNU Parallel, but you are using the command line, then you should consider spending 15 minutes on ...
ngs parallel tool written 4 months ago by ole.tange3.4k
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Comment: C: how to add the sample name to the end read headers
... Can you elaborate in why you do not have that? Is your reason covered on https://oletange.wordpress.com/2018/03/28/excuses-for-not-installing-gnu-parallel/ ...
written 6 months ago by ole.tange3.4k
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Answer: A: HOMER parallel annotation for big .bed file
... Can you test if this works, too: parallel -a ../Big_bed.bed --pipe-part --block -1 --fifo \ annotatePeaks.pl {} hg19 > ./../anno_chunks/{.}_annotated.txt or this (slower): parallel -a ../Big_bed.bed --pipe-part --block -1 --cat \ annotatePeaks.pl {} hg19 > ./../anno_chun ...
written 8 months ago by ole.tange3.4k
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Comment: C: Trim_galore on multiple fast.qz files: syntax problem
... `find` is used because OP used `find`. Your solution will often give the same result, but will fail if the files are in subdirs inside path_to_fastq or if there are so many that they do not fit on a single command line. ...
written 8 months ago by ole.tange3.4k
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Answer: A: Trim_galore on multiple fast.qz files: syntax problem
... This: find path_to_fastq -name "*_R1_001.fastq.gz" | parallel -j 1 trim_galore --paired --fastqc -o trim_galore/ {} {= s/_R1_/_R2_/ =} or: find path_to_fastq -name "*_R1_001.fastq.gz" | parallel --plus -j 1 trim_galore --paired --fastqc -o trim_galore/ {} {/_R1_/_R2_} ...
written 8 months ago by ole.tange3.4k

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