My supervisor has requested that I create coverage plots to visualize BAM alignments of RNA-Seq data. I though a good way to do this would be to use Gviz. We work on the model legume Medicago truncatula which does not have a BSgenome package so I though I'd try and make one.
Following the vignette I have placed all the chromosomes in their own FASTA files and gziped them. I then created a seed file like so:
Title: Full genome sequences for Medicago truncatula A17 (JCVI version 4)
Description: Full genome sequences for Medicago truncatula A17 (Barrell medic) as provided by JCVI (v4, 2014) and stored in Biostrings objects. See Tang et al. (2014) BMC Genomics 15:312
organism: Medicago truncatula A17
common_name: Barrell medic
seqnames: c(paste0("Medtr4_0_", "chr",1:8), paste0("Medtr4_0_", "scaffold",sprintf("%04d", 1:2179)))
However when I run
forgeBSgenomeDataPkg() i get this error:
Creating package in ./BSgenome.Mtruncatula.JCVI.v4 Error in getSeqSrcpaths(seqname, prefix = prefix, suffix = suffix, seqs_srcdir = seqs_srcdir) : file(s) not found: /home/gthomson/Documents/Scratch/Alignment_visualisation/Medtr4_0.tar.gz/Medtr4_0_chr1.fa
This is weird because I can look at this folder and it is there:
How can I do this and any easier methods to generate coverage plots are welcome.