Hello all.
I have been trying to do a Reference-based assembly for my RNA-seq data. It is Illumina paired-end data of 100bp reads.
There are 8 different sets of data samples.
But now I have a problem for aligned the reads to the reference. I have the fasta sequence of contigs, scaffolgs, genes and complete mRNA. The sequences are split in the form of chromosomes. This data was downloaded from an already available browser, with view in Chromosome-wise.
I plan to use Bowtie for the alignment, and I need a new Index for my genome as its not readily available.
Which is the reference for Transcriptome alignment - contigs, scaffolgs, genes, complete mRNA or something else?
I tried using contigs, mRNA, scaffold fasta sequences but only 0.05% of the reads align to any of these.
What exactly must be used as the reference? What should the Bowtie Index be built upon???
My aim is to create the BAM files so that it can be viewed in the Genome Browser.
I have been trying to do a Reference-based assembly for my RNA-seq data. It is Illumina paired-end data of 100bp reads.
There are 8 different sets of data samples.
But now I have a problem for aligned the reads to the reference. I have the fasta sequence of contigs, scaffolgs, genes and complete mRNA. The sequences are split in the form of chromosomes. This data was downloaded from an already available browser, with view in Chromosome-wise.
I plan to use Bowtie for the alignment, and I need a new Index for my genome as its not readily available.
Which is the reference for Transcriptome alignment - contigs, scaffolgs, genes, complete mRNA or something else?
I tried using contigs, mRNA, scaffold fasta sequences but only 0.05% of the reads align to any of these.
What exactly must be used as the reference? What should the Bowtie Index be built upon???
My aim is to create the BAM files so that it can be viewed in the Genome Browser.
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