Hi Dear Friends, ( I'm not native in English so, be ready for some possible language flaws)
I have 6 paired end 100 bp fastq files (3 for female and 3 for males, paired-end reads = 12 files) which is from Illumina HiSeq RNA_seq process of a non-model fish. I have run some de novo transcriptome assembly using Trinity package.
Now I want to do some genome-guided investigation on the same data to check for the annotation of transcripts that did not show any blast hit in de novo assembly.
So, I have downloaded a close species reference genome from NCBI.
Now I want to map my reads to that genome.
1- which splice aware aligner is preferred ? STAR or BBmap ?
2- in the old "bowtie --> tophat --> cufflink" pipeline, it must be some "bowtiebuild" preparing the reference genome file, is it needed yet ?
3- can I use all my 12 files in just one command ? or I must use sample1-lef - sample1-right maping first and then repeat it for other 5 files ?
please share any useful script for aligning that you think it would be useful.
Thank you in advance