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ChrisR/NextGenSeq tools

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< User:ChrisR

This page collects work-flows to work with big data from NextGenSequencing, mainly from population genetics studies including on ancient DNA. The focus is on Y-chromosomes to research variants and haplogroups.

Data collection and extraction of the needed data portions

To avoid the need of high bandwidth traffic the use of online tools is very handy.

Biostars Galaxy

After a registration this online tool can be used to handle big NGS data available trough online servers:

  • Select from Menu: "Get Data > Upload File" and upload the data file (BAM)
  • NGS: SAMtools > Slice BAM by genomic regions > by chromosomes/contigs > Y
  • NGS: SAMtools > Sort BAM dataset > chromosomal coordinates (often the data is already sorted but this step does no harm if repeated)
  • Edit attributes to Rename the file and add a description, save the file in history
  • click on the file to download BAM/BAI or directly open it in IGV or IGB Viewers
  • use SNP bed files to browse if variant positions have calls and are positive