I have nine RNA-Seq files that I aligned using the hisat2 aligner and this default command:
hisat2 -x grch37_snp_tran/genome_snp_tran -1 reads_R.fastq.gz -2 reads_F.fastq.gz -S sample.sam
The -x file was the one they recommened in the hisat2 website.
Files looked fine and I proceed to the bam, sorted bam and bai using samtools.
However, when I use stringtie with this command:
stringtie file.sorted.bam -G Homo.sapiens.GRCh37.75.gtf -o file.gtf
It happens that in some sample I am losing genes as important as CCND1, while I keep them in other files. It is very strange as I have some transcripts with zero coverage/FPKM/TPM, so I expected that they were in my file.gtf. Am I doing something wrong? If I use the same command for all the samples, how can it be that I lose this transcript in one but not in others? In addition, how it can be that I don't have the same number of genes in all my generated files if I am using the same Homo.sapiens.GRCh37.75.gtf?