I am using the line below to convert SAM to BAM and then sort them:
samtools view -bS $mySAM | samtools sort -n -m 6000000000 - $myBAM
Eventhough the process seem to be generating an output, I receive the following log:
[bam_header_read] EOF marker is absent. The input is probably truncated. [samopen] SAM header is present: 211 sequences.
Is the fact that I am inputting an aligned RNASeq.sam file and it indicates that 211 sequences have SAM header something I need to worry about?
I appreciate your feedback,