Hello everyone.
I run bisulfite sequencing mapping with BSMAP. The output file was .sam format.
But the quality scores look very strange. There were lots of unknown characters(I attached a picture)
Here is the script:
./bsmap -a B4_ATGTCA_L00${i}_R1_00${j}.fastq -b B4_ATGTCA_L00${i}_R2_00${j}.fastq -d hg19.fa -o B4_ATGTCA_L00${i}_00${j}.sam -z 64 -v 15 -x 1000
Did I do something wrong or set up wrong parameter?
Thank you so much in advance!
I run bisulfite sequencing mapping with BSMAP. The output file was .sam format.
But the quality scores look very strange. There were lots of unknown characters(I attached a picture)
Here is the script:
./bsmap -a B4_ATGTCA_L00${i}_R1_00${j}.fastq -b B4_ATGTCA_L00${i}_R2_00${j}.fastq -d hg19.fa -o B4_ATGTCA_L00${i}_00${j}.sam -z 64 -v 15 -x 1000
Did I do something wrong or set up wrong parameter?
Thank you so much in advance!
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