title: Ashwellthorpe2 (AT2) variants from RNA-seq reads alignment against v1 KW1 contigs
organism: Hymenoscyphus fraxineus
description: Variant analysis of RNA-Seq data of a fungla infected sample isolated from Ashwellthorpe2 (AT2), Norfolk, England. RNA_seq reads from AT2 are aligned to Kenninghall wood (KW1) version 1 contigs (available at https://github.com/ash-dieback-crowdsource/data/blob/master/ash_dieback/chalara_fraxinea/Kenninghall_wood_KW1/assemblies/gDNA/KW1_assembly_version1/Chalara_fraxinea_TGAC_s1v1_contigs.fa) using BWA mem v 0.7.4 and Samtools 0.1.17 was used to generate variants. Since Samtools 0.1.17, doesn't generate contig names in the header, such a header was incorporated from a file generated using samtools 0.1.19. Contig/chromosome names are required to submit vcf files on ENA.
attributes.tag: ENA first public
attributes.value: 2015-03-25
attributes.tag: ENA last update
attributes.value: 2015-03-25
attributes.tag: External Id
attributes.value: SAMEA3313345
attributes.tag: INSDC center alias
attributes.value: THE SAINSBURY LABORATORY
attributes.tag: INSDC center name
attributes.value: THE SAINSBURY LABORATORY
attributes.tag: INSDC first public
attributes.value: 2015-03-25T17:01:42Z
attributes.tag: INSDC last update
attributes.value: 2015-03-25T11:01:54Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: AT2_RNA-Seq Variants
attributes.tag: sample name
attributes.value: AT2_RNA-Seq Variants