Results for "tmp"
Blogs
...string # must match exactly, so use a variable: outfile = "/tmp/foobar.txt"; print "fo...# Reads a line from a file and stores in localvar infile = "/tmp/foobar.txt"; getline loc...1848 days ago
- ...how job=<jobid> 4. Cancel a jobTo cancel one job: scancel <jobid> To cancel one job and delete the TMP directory created by the subm...
682 days ago
Bookmarks
splitbam: splits a BAM by chromosomes
...file/bam pattern) REQUIRED. MUST contain __CHROM__ and end with .bam -s assume input is sorted. -x | --index create index. -t | --tmp (dir) tmp file directory -G (file) chr...2636 days ago
Pages
Find certain files/documents in Linux OS
.... Find all Empty FilesTo file all empty files under certain path.# find /tmp -type f -empty20. Find all Empty DirectoriesTo file all empty directories under certain path.# find /tmp -type d -empty21. File all Hi...3694 days ago
Linux Sort Commands for Bioinformatics
...ed on its first column, then the second if the first is the same, and so on:sort input.txt sort a huge file (GNU sort ONLY):sort -S 1500M -t $HOME/tmp input.txt > sorted.txt so...3640 days ago
Top-level pages
- ...rminates if exceeded) [default: 250] --tmp-dir <dirname>...rary files [default: <output_dir>/tmp] -k <int,int...
2364 days ago
- ...sing=True, norearrangements=False, noreduction=True, noscaffolding=True, outdir='test/run1', overlap=0.8, reference='', resume=False, threads=4, tmp='/tmp', usebwa=False, verbose=True)...
2203 days ago
- +1 more Top-level pages
Wire posts
Bio-Scripts
Insert the sequence at desire location in multi-fasta file with Perl
#!/usr/bin/perl use warnings; use strict; use Bio::SeqIO; use Bio::Seq; use File::Copy; #ARGV[0] should be in following format --- Keep the coordinate sorte...2327 days ago
Perl script to read multi fasta sequence one by one
#!/usr/bin/env perl use strict; use warnings; #USAGE #perl rohanRun.pl seq.fa my $outfile='tmp.fa'; my $fastaSeq_ref = readfasta ("$ARGV[0]"); my %fastaSeq = %$fastaSeq_r...2234 days ago
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Comments
Comment on "Nanopolis: polish a genome assembly"
...raft.fa # Align the basecalled reads to the draft sequence bwa mem -x ont2d -t 8 draft.fa reads.fa | samtools sort -o reads.sorted.bam -T reads.tmp - samtools index reads.sorte...2112 days ago
- ...----- -t INT : Number of threads (<= 100, default 1) -o STR : Prefix of output files (default out, length <= 200) -tmp DIR : directory for temporar...
2812 days ago
