I'm mapping 36bp single ended reads to C.elegans cDNA reference by bwa, trying to make variant calling after getting mpileup files. The problem is the samtools mpileup doesn't work well with my reference sequence and show all Ns in the third column.
Like this:
AC8.4 3 N 1 ^!G I
AC8.4 4 N 1 A I
AC8.4 5 N 1 A I
AC8.4 6 N 1 T I
AC8.4 7 N 1 G I
AC8.4 8 N 1 C I
Do you know what's wrong?
P.S. my reference consists of 55783 chromosomes (transcripts), each one with about 20~10k bp length.
My commanding lines are like this:
bwa -n 1 -t 7 -l 10000 -o 0 XXX.fa XXX.fastq > XXX.sai
bwa samse -n 10 XXX.fa XXX.sai XXXfastq > XXX.sam
samtools view -S -b XXX.sam > XXX.bam
samtools sort XXX.bam XXX_sorted
samtools mpileup -f XXX.fa XXX_sorted.bam > result.mpileup
Plz help me, thank you very much!
Like this:
AC8.4 3 N 1 ^!G I
AC8.4 4 N 1 A I
AC8.4 5 N 1 A I
AC8.4 6 N 1 T I
AC8.4 7 N 1 G I
AC8.4 8 N 1 C I
Do you know what's wrong?
P.S. my reference consists of 55783 chromosomes (transcripts), each one with about 20~10k bp length.
My commanding lines are like this:
bwa -n 1 -t 7 -l 10000 -o 0 XXX.fa XXX.fastq > XXX.sai
bwa samse -n 10 XXX.fa XXX.sai XXXfastq > XXX.sam
samtools view -S -b XXX.sam > XXX.bam
samtools sort XXX.bam XXX_sorted
samtools mpileup -f XXX.fa XXX_sorted.bam > result.mpileup
Plz help me, thank you very much!
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