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I used pysam to treat a NGS primarily mapped bam and found the aligned chromosomes of some reads were started #, but with the code read.reference_name it displayed the correct chromosome. Here is one example of these reads.
for record in bam.fetch():
if record.query_name == "c4e0190a-6474-4007-997b-d868cf363f4e":`
read = record
print(read)
Here is a sam file containing the read c4e0190a-6474-4007-997b-d868cf363f4e. testsam.zip
Could you clarify the reason for the use of # to denote chromosomes in pysam? Looking forward to your reply.
The text was updated successfully, but these errors were encountered:
Hello,
I used pysam to treat a NGS primarily mapped bam and found the aligned chromosomes of some reads were started
#
, but with the coderead.reference_name
it displayed the correct chromosome. Here is one example of these reads.print(read.reference_name)
When I checked this read using
samtools view
, it displayed the correct chromosome,Here is a sam file containing the read
c4e0190a-6474-4007-997b-d868cf363f4e
. testsam.zipCould you clarify the reason for the use of
#
to denote chromosomes in pysam? Looking forward to your reply.The text was updated successfully, but these errors were encountered: