I have 6 wheat samples sequenced using RNA-seq. I received forward and reverse fastq files and I generated bam files by using hisat2 tool which are aligned with the reference wheat genome. I have been asked to build multiple sequence alignment for 3 genes from this sequenced rna seq data. I believe I need to select a gene sequence from all the samples and do a multiple sequence alignment. But I am struck in fetching the gene sequence from bam files. How do I select one gene sequence for all the 6 samples? Any suggestions? kidly send me commands for fetching the sequence of genes from this RNA seq data in fastq file or aligned.bam file.
Hi Buffo, Thanks, I have run the srtigtie.got this error. kindly check this error.i did not get it and solve it .Kindly set this commandaccording to my sample.
./stringtie G1_sorted.bam -B -o G1.gtf -G Triticum_aestivum.IWGSC.42.gtf -p 4 -C G1.refs.gtf -A G1.abund.tab -WARNING: no reference transcripts were found for the genomic sequences where reads were mapped! Please make sure the -G annotation file uses the same naming convention for the genome sequences