So, I received fastq files that were marked as fastq_passed. There was a folder for fastq_failed that I ignored. Next, I concatenated all of the fastq files using linux command cat *.fastq >final_file.fastq I then downloaded hg19 reference genome, and aligned this concatenated fastq file using minimap2, specifically using command for RNA data. I sorted and converted to bam. I quickly looked at the data using samtools view, and noticed that all the columns were either Chr1 and Chr M. Most of then appeared to be *, if I remember correctly. So I ran featurecounts using the inbuilt hg19. Most of the ids had count of 0, with two(both mitochondrial) having count of 1. I also downloaded a lncrna specific gtf file and ran featurecounts. In this case, the counts were all zeros . I am thinking that I am doing something incorrectly. Any ideas? The BAM file is around 600M. The concatenated fastq file uncompressed is 1.2G. One would think that there would be some data. What reference genome do I use for Lncrna? What about gtf file. The project requires that I use hg19.
Thanks.
