where i can download reference MSU7 rice genome?

Question

[PK]

I am working with RNA Seq data analysis. I have to download MSU7 rice genome. somehow i downloaded from (http://rice.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/all.dir/) But i am not able to find Annotation (.gtf) file and reference genome (.fa) file . so how can i find and how can i download. Another question is how to define (--frag-len-mean 262 --frag-len-std-dev 80 ) these two things for oryza sativa (how much i need to give mean and std-dev). help me

[Denise CS]

In Ensembl Plants, you can download the gtf and the fasta files from their FTP. The assembly there is a "a unified assembly of the 12 rice pseudomolecules of Oryza sativa Japonica Group cv. Nipponbare by scientists from the MSU Rice Genome Annotation Project (MSU) and the International Rice Genome Sequencing Project (IRGSP) / Rice Annotation Project Database (RAP-DB).

Answer 1

[GenoMax]

At the MSU link included your post, this file (rather strangely named all.con) appears to have the sequence of the chromosomes. There is also this GFF file for annotation.

[PK]

Thank you very much. I have another doubt. This cufflinks program for human " cufflinks -p 8 -o HBR_Rep1_ERCC-Mix2 --library-type fr-firststrand --GTF $RNA_HOME/refs/hg19/genes/genes_chr22_ERCC92.gtf --frag-len-mean 262 --frag-len-std-dev 80 --no-update-check $RNA_HOME/alignments/tophat/HBR_Rep1_ERCC-Mix2/accepted_hits.bam ". My doubt is i have to do for rice so i have to change anything or not.

[GenoMax]

You would need to use your own annotation and alignment files. You can use the gffread utility in cufflinks to convert the GFF file into GTF (something like gffread my.gff3 -T -o my.gtf). If you don't know the frag lengths I think you can omit those options.

[PK]

Thanks for your reply. Is there any way to find frag lengths.

[GenoMax]

You could using bbmerge.sh from BBMap suite.

1) Via mapping, which requires a reference: bbmap.sh in1=r1.fastq in2=r2.fastq ref=ref.fasta ihist=ihist.txt reads=2m pairlen=2000

2) Via overlap, which requires overlapping reads: bbmerge.sh in1=r1.fastq in2=r2.fastq ihist=ihist.txt reads=2m

[PK]

Thanks for your help