question in “Map the data to the reference genome” step

[L1angyan]

Hi Zijie,

I notice that when you mapping reads to the ref genome, you use the parameter: -k 1

hisat2 -x $INDEX --known-splicesite-infile $SPLICE -k 1 --no-unal --summary-file $s.IN.align_summary -p 4 -U $Data/$s.IN.noMyco.fastq.gz |samtools view -bS |samtools sort -o $Output/$s.input.bam

hisat2 -x $INDEX --known-splicesite-infile $SPLICE -k 1  --no-unal --summary-file $s.m6A.align_summary -p 4 -U $Data/$s.m6A.noMyco.fastq.gz | samtools view -bS |samtools sort -o $Output/$s.m6A.bam

However, it could lead to reads mapping to a inappropriate region, because it match k=1.

looking foward your reply
Liangyan

[L1angyan]

If you use -k 1, a read maybe map to a not so appropriate position but meet the criteria of finding 1 alignment.