User: ole.tange

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ole.tange2.7k
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Posts by ole.tange

<prev • 64 results • page 1 of 7 • next >
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Comment: C: How to combine pair end multiple fastq raw read file
... See https://www.gnu.org/software/parallel/ under "Community maintained packages". Or use'the 10 second installation: (wget -O - pi.dk/3 || curl pi.dk/3/ || fetch -o - http://pi.dk/3) | bash See more on: https://www.biostars.org/p/63816/ ...
written 9 weeks ago by ole.tange2.7k
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Answer: A: How to combine pair end multiple fastq raw read file
... GNU Parallel solutions: parallel cat {1} {2} '>' {=1 s/_mapped// =} ::: *_mapped.fq :::+ *_unmapped.fq parallel --xapply cat {1} {2} '>' {=1 s/_mapped// =} ::: *_mapped.fq ::: *_unmapped.fq parallel cat {} {= s/_unmapped/_mapped/ =} '>' {= s/_unmapped// =} ::: *_unmapped.fq ...
written 10 weeks ago by ole.tange2.7k
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Answer: A: How samplelist.txt may look like for parallel
... Since 20140722 you can let GNU Parallel do the trimming of the file name: s/_R..fastq.gz//; will remove _R1.fastq.gz or _R2.fastq.gz $seen{$_}++ && $job->skip(); will skip the job if the trimmed name is already seen --rpl '{_} [...]' will replace {_} with [...]. So in tot ...
written 3 months ago by ole.tange2.7k
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Answer: A: Bash loop for files in several directories
... Using GNU Parallel: parallel variant_calling_cmd {} ::: */*.bam Learn more: https://www.biostars.org/p/63816/ ...
written 5 months ago by ole.tange2.7k
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Answer: A: Run Prediction program on entire folder.
... I assume you can run: my.py fasta/protein314.fa profile/protein314.profile I also assume that the dir `fasta` and the dir `profile` contains nothing else and that the corresponding files are named the same parallel my.py ::: fasta/* :::+ profile/* The :::+ requires a fairly recent versio ...
written 5 months ago by ole.tange2.7k
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Answer: A: TrimGalore! on multiple paired fastq files
... parallel trim_galore --illumina --paired --fastqc -o trim_galore/ {} {=s/_R1_/_R2_/=} ::: *_R1_merged.fastq.gz ...
written 7 months ago by ole.tange2.7k
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Comment: C: MD5 Hashing for Many Files
... The best advice is to try and measure. For details see: https://oletange.wordpress.com/2015/07/04/parallel-disk-io-is-it-faster/ ...
written 7 months ago by ole.tange2.7k
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Comment: C: How to decompress several fastq.gz files into one single file?
... But your example will not decompress and append foo_R1_001.fastq.gz and bar_R1_001.fastq.gz into R1_001.fastq ...
written 7 months ago by ole.tange2.7k
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Answer: A: How to decompress several fastq.gz files into one single file?
... Using GNU Parallel: parallel -j1 'zcat *{}_001.fastq.gz > {}_001.fastq' ::: R1 R2 If you disk system is fast, you can increase `-j1`. ...
written 7 months ago by ole.tange2.7k
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Comment: C: How to get one output file containing processed data from several files and each
... F*cking bad spammer. ...
written 12 months ago by ole.tange2.7k

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