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.
where i can download reference MSU7 rice genome?
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
1 answer
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.
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
Log in to answer this question.
More posts like this
-
Enrichment analysis guide for msu7 rice genome
written by sumitra.20 •
-
Reference genome for oryza sativa indica group
written by sumitra.20 •
-
Subread FeatureCounts produces zero percent successfull alignment
written by mathavanbioinfo
-
How to use MSU7 rice genome as reference as there has fasta file format.
written by Mainul •
-
transcript assembling problem by cufflinks
written by kuhelikadas1995 •
-
For only a few genes, Cuffdiff report more than one FPKM values per locus. Why?
written by rice.researcher
-
RNA-Seq tophat command error?
written by PK •
-
How to specify frag len mean and frag len std dev while running cufflinks?
written by PK •
-
Error: gtf_to_fasta returned an erro - Is there any better Rice gtf file for RNAseq is available?
written by kozhaki.seq
-
Gff Parsing In Biopython Is Not So Perfect
written by Gahoo
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).