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
2319 days ago
Tags: VCFtools, Perl, API, Vcf.pm, Perl, scripts, VCF, validation, file, merging, intersecting, complements
2086 days ago
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
2006 days ago
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
1978 days ago
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.faTags: dictionary, next, reference, file, samtools, SAMException
1532 days ago
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
1492 days ago