I am newbie working on RNA-Seq analysis. I have samples processed using Illumina RNA Exome and Illumina TrueSEq librray protocols Paired end. I initially dif the qulaity control and I dont see any adpater contamination. I trimmed first 15 random reads and performed alignment step using STAR aligner. The samples are human so I aligned against hg38 reference genome. But the alignment is low. I have got around 64% uniquely mapped reads. I am not sure if this is rRNA contamination considering that the two library protocols lack the rRNA depletion step. I was trying to output the unmapped reads using OutReadsUnmapped Fastx. The output I get when I use the above option is unmapped.out.mate1 and unmapped.out.mate2. I am not sure if these are sam files or bam files or fastq files. From the manual I see that you get either fasta or fastq files. But I just see unmapped.out.mate1 and unamapped.out.mate2. I am trying to run blast on these unmapped reads to see if anything matches. Could somebody help me with converting the unmapped.out.mate1 file to fastq file?
Thanks in advance.