Hi,
I have mRNA sequencing data, from low amount of cells using SMARTer kit and Illumina GA, 36 single end reads.
I mapped them with gsnap to mouse mm10 genome and got count table with HTSeq. 75% of reads mapped to genome, but only 35% mapped to exons, while as much as 40% to 'no feature'.
Before I was analysing similar data, also obtained from little amount of cells with SMARTer kit (but 75bp PE reads) and I was 85% reads mapped, while only 10% mapped to 'no feature'.
Did anyone experience that? Where should I look for problems? Could it be DNA contamination of the sample? Or maybe problem lies somewhere in mapping?
my commands were:
gsnap -A sam -B 5 -t 10 -n 1 -Q --nofails –D /path/path/mouse -d mouse -s mouse sample.fq > sample.sam
htseq-count sample.sam /path/path/Mus_musculus.GRCm38.70.gtf > sample.txt
Thanks
I have mRNA sequencing data, from low amount of cells using SMARTer kit and Illumina GA, 36 single end reads.
I mapped them with gsnap to mouse mm10 genome and got count table with HTSeq. 75% of reads mapped to genome, but only 35% mapped to exons, while as much as 40% to 'no feature'.
Before I was analysing similar data, also obtained from little amount of cells with SMARTer kit (but 75bp PE reads) and I was 85% reads mapped, while only 10% mapped to 'no feature'.
Did anyone experience that? Where should I look for problems? Could it be DNA contamination of the sample? Or maybe problem lies somewhere in mapping?
my commands were:
gsnap -A sam -B 5 -t 10 -n 1 -Q --nofails –D /path/path/mouse -d mouse -s mouse sample.fq > sample.sam
htseq-count sample.sam /path/path/Mus_musculus.GRCm38.70.gtf > sample.txt
Thanks