I'm stuck at the path where I'm about to call mitochondrial region (ChrM) from the whole genome sequencing data.
I have gone through the fastq, alignment and now I'm going deeper; calling ChrM out (because I'm specifically want to use mitochondrial region only for my study).
What I did was;
1) I have sorted .bam file, the command was like:
samtools sort unsorted_in.bam sorted_out
2) Then I converted the sorted .bam file into .sam. The command was:
samtools view -h file.bam > file.sam
3) After that, I have indexed sorted.bam file and the command was:
samtools index sorted.bam
Everything seems okay until I run the command to call ChrM region. The command for calling ChrM that I have used was this one:
samtools view -h sorted.bam | awk '$3== "chrM" || /n@/' | samtools view -Sb -> chrM.bam.sorted.bam
So, I typed this in the terminal and it appeared:
ws04@empress:/srv/disk01/Tools/samtools-0.1.19$ samtools view -h /srv/disk01/Postgraduates/OrangAsli/KS12R/Alignments/KS12R_sorted.bam.bam | awk '$3=="chrM" || /n@/' | samtools view -Sb -> /srv/disk01/Postgraduates/OrangAsli/KS12R/ChrM/KS12R_chrM.bam.sorted.bam [samopen] no @SQ lines in the header. [sam_read1] missing header? Abort!
I have tried more than twice but it's still the same. What does it mean with 'no @SQ lines in the header?'
I hope you guys can help me. Thank you in advance and glad to hear from you guys soon.
Thanks again, Lynn.