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• converting SAMRecord to JSON or String format
  I want to develop RESTful web service which will provide bam reads in JSON format. I used SamFile...
• Error with String data base CYTOSCAPE
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• Converting dot to json
  Hi, I have a pan-genome graph file in dot format, anybody knows how to convert graph file in dot...
• Why annotations are not encoded using standard informatic format ?
  Hi, I don't know if this kind of question can be asked on BioStar. I quite don't understand why,...
• Converting UUID downloaded from GDC to TCGA names
  hi! I have dwnloaaded files regarding breast cancer genome transcription with the following pytho...
• VEP JSON output parsing
  I'm writing a python parser for VEP produced serialised JSON output, but finding the alleles reco...
• Download all SRA of one species
  I try to run the code below #!/usr/bin/python2.7 import json, urllib query = '"Vibrio cholerae...
• Conventions for sorting provenance (original URL, processing steps) in VCF file
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• Querying VEP using REST API
  I'd like to query a JSON output for VEP using the REST API. I have the following code in python ...
• VCF annotations -> readable info using PyVCF?
  Hey, so I am working on a script that will run a VCF through several different databases for anno...
• Samtools: Why Have I Been Using "View" Command For Mpileup
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• Create a File format to store Variant
  Hi, BED format or VCF format are not well designed to store [hgvs][1] notation and metadatas of ...
• Should We Be Using Much More Json In Our Delimited Data Formats?
  Many bioinformatic files are delimited because delimited files are so useful for manipulation and...
• How To Specify Positional Argument Order In A Gkno Tool
  Hi, I'm integrating a custom tool into gkno. My tool uses positional arguments that need to be i...
• tximeta error (coldata)
  Hello. I am trying to use tximeta package. I have quant.sf files from salmon. my code is the foll...
• Sorting samtools output by flag or grepping its tags
  Hi! I am getting confused with couple samtools outputs. I have run bwa-mem with -M flag to retri...
• Obtaining input matrix from Kallisto for later downstream analysis with Deseq2 or EdgeR.
  Dear All! I am very new to bioinformatics and trying to connect phenotype of certain cells with...