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• • Rahul Nayak@rahul

  

  Remove unwanted character from fasta file. sed -e '/^[^>]/s/[^ATGCatgc]/N/g' file.fa #fasta #file #header #charater

  Tags: fasta, file, header, charater

  2473 days ago

• • Jit@jit.aber

  

  Sort a file with column 2: sort -g -k 2,2 allPacbio.fa.fai > sorted.fai #sort #file #column

  Tags: sort, file, column

  2360 days ago

• • Jit@jit.aber

  

  Biological file format tutorial

  This section explains some of the commonly used file formats in bioinformatics. The information provided here is basic and designed to help users to distinguish the difference between different formats. Please refer user manual or other information resources on web for more details. FASTA FAS...

  Tags: Biological, file, format, tutorial

  2322 days ago

• • Jit@jit.aber

  

  Find matching file names with pattern in a directory. $ ls -dq *_name2search_* | wc -l #file #search #hits #pattern #names #directory

  Tags: file, search, hits, pattern, names, directory

  2229 days ago

• • Rahul Nayak@rahul

  

  VCFtools: perform common tasks with VCF files such as file validation, file merging, intersecting, complements

  VCFtools contains a Perl API (Vcf.pm) and a number of Perl scripts that can be used to perform common tasks with VCF files such as file validation, file merging, intersecting, complements, etc. The Perl tools support all versions of the VCF specification (3.2, 3.3, 4.0, 4.1 and 4.2), nevertheless...

  Tags: VCFtools, Perl, API, Vcf.pm, Perl, scripts, VCF, validation, file, merging, intersecting, complements

  2089 days ago

• • Neelam Jha@neelam

  

  UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte

  whatshap phase -o seeWhat.vcf --reference genome.fa see.vcf genome.fa.sorted.bam This is WhatsHap 0.17 running under Python 3.6.6Traceback (most recent call last): File "/home/anaconda3/bin/whatshap", line 11, in <module> load_entry_point('whatshap==0.17', 'console_scripts', 'whatshap')(...

  Tags: whatshap, error, invalid, file

  2010 days ago

• • BioJoker@biojoker

  

  Understating pacbio reads name !

  m140415_143853_42175_c100635972550000001823121909121417_s1_p0/553/3100_11230 0.99 24 └1┘└─────2─────┘└──3─┘└────────────────4────────────────┘└5┘└6┘└7┘└────8────┘└─9─┘└10┘ "m" = movie Time of Run Start (yymmdd_hhmmss) Instrument Serial Number SMRT Cell Barcode Set Number (a.k.a. "L...

  Tags: pacbio, file, name, explanation

  1981 days ago

• • BioJoker@biojoker

  

  To know about the file detail $ file .face #file #detail

  Tags: file, detail

  1925 days ago

• • Rahul Nayak@rahul

  

  Error: Could not find dictionary next to reference file file

  htsjdk.samtools.SAMException: Could not find dictionary next to reference file file:///data/sata_data/workshop/wsu29/Parivartan/snakemake_germline_legacy/references/GRCh38.primary_assembly.genome.fa

  Tags: dictionary, next, reference, file, samtools, SAMException

  1536 days ago

• • Jit@jit.aber

  

  tinycov: standalone command line utility written in python to plot coverage from a BAM file

  Tinycov is a small standalone command line utility written in python to plot the coverage of a BAM file quickly. This software was inspired by Matt Edwards' genome coverage plotter. To install the stable version: pip3 install --user tinycov To install the development version: git clo...

  Tags: tinycov, standalone, command, line, utility, written, python, plot, coverage, BAM, file

  1496 days ago

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