I did an aligment with STAR, I got the sam file which I can open easily from the terminal:
samtools view -S STAR2Aligned.out.sam
Now I have to work with it in python, so I import the pysam module and try to open the file by:
file = pysam.AlignmentFile("/home/lpp/Desktop/Star_Results/STAR2Aligned.out.sam", "r")
it prints the following error:
[W::sam_hdr_parse] duplicated sequence 'NODE_4_length_21_cov_1.000000'
[W::sam_hdr_parse] duplicated sequence 'NODE_18_length_23_cov_1.000000'
I tried to find the error in different forums but the most similar one to my problem has no answer:
Does anybody now where this error is coming from?
thanks in advantage!