Open Access Highly Accessed Research article

Use of mRNA-seq to discriminate contributions to the transcriptome from the constituent genomes of the polyploid crop species Brassica napus

Janet Higgins12, Andreas Magusin1, Martin Trick1, Fiona Fraser1 and Ian Bancroft1*

Author Affiliations

1 John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK

2 The Genome Analysis Centre, Norwich Research Park, Norwich, NR4 7UH, UK

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BMC Genomics 2012, 13:247  doi:10.1186/1471-2164-13-247

Published: 15 June 2012

Additional files

Additional file 1:

Perl program (tagcounter.pl) to parse a MAQ “pileup” file and count the number of reads mapping to each unigene, outputting a read count and calculated RPKM.

Format: TXT Size: 3KB Download file

Open Data

Additional file 2:

Perl program (Illumina_split_read.pl) to split 80 base Illumina FASTQ reads into 2 files containing the first 40 base and last 40 base of each read.

Format: TXT Size: 2KB Download file

Open Data

Additional file 3:

Perl program (cure_cycle_split.pl) calling MAQ to align reads to a reference, then calling cure_refseqs.pl to perform curing of the reference sequence over a specified number of cycles.

Format: TXT Size: 2KB Download file

Open Data

Additional file 4:

Perl program (cure_refseqs.pl) to “cure” the naive reference using the consensus sequence obtained from alignment of reads from target genome.

Format: TXT Size: 3KB Download file

Open Data

Additional file 5:

Perl program (compare_sequences.pl) to compare two sequences and output a list of positions at which base differences occur together with the base call.

Format: TXT Size: 2KB Download file

Open Data

Additional file 6:

Perl program (ACtagcounter.pl) to parse and Illumina “pileup” file and count reads for the A and C version of each unigene, outputting a read count and calculated RPKM.

Format: TXT Size: 3KB Download file

Open Data