User: ole.tange
ole.tange • 2.7k
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Posts by ole.tange
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2
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5
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168
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5
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Comment:
C: Run Samtools on multiple files
... --eta implies --progress, so --progress is not needed. Also try the newer --bar. If you want one per cpu core, leave out -j8. ...
written 20 hours ago by
ole.tange • 2.7k
1
vote
2
answers
257
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2
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... 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 3 months ago by
ole.tange • 2.7k
2
votes
2
answers
257
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2
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... 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 3 months ago by
ole.tange • 2.7k
2
votes
3
answers
225
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3
answers
... 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 4 months ago by
ole.tange • 2.7k
1
vote
4
answers
343
views
4
answers
... Using GNU Parallel:
parallel variant_calling_cmd {} ::: */*.bam
Learn more:
https://www.biostars.org/p/63816/
...
written 6 months ago by
ole.tange • 2.7k
1
vote
1
answer
263
views
1
answers
... 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 6 months ago by
ole.tange • 2.7k
0
votes
1
answer
415
views
1
answers
... parallel trim_galore --illumina --paired --fastqc -o trim_galore/ {} {=s/_R1_/_R2_/=} ::: *_R1_merged.fastq.gz
...
written 8 months ago by
ole.tange • 2.7k
0
votes
0
answers
311
views
0
answers
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 8 months ago by
ole.tange • 2.7k
0
votes
4
answers
760
views
4
answers
... But your example will not decompress and append foo_R1_001.fastq.gz and bar_R1_001.fastq.gz into R1_001.fastq ...
written 8 months ago by
ole.tange • 2.7k
1
vote
4
answers
760
views
4
answers
... Using GNU Parallel:
parallel -j1 'zcat *{}_001.fastq.gz > {}_001.fastq' ::: R1 R2
If you disk system is fast, you can increase `-j1`.
...
written 8 months ago by
ole.tange • 2.7k
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