I have Fastq reads something like
@HWI-ST1162:73:C0KEFACXX:6:1101:1816:1918 1:N:0:CGATGT NACCCTAGAAATTATAAATCTCTTCAAGTGAGATTGTAAGGAGAAGGAGAAACTTGGTCTGGAATTTGTTATAAAAGCACTT + #1=DDFFFHHGGHIJJJJJIJJJJJJJJCHGHIIJJEFHIJIJJIIJIIIIJHHIJJFHIIJJJJJJJIJIJIJIIJHEHHHHFFFFFFEEEDEEEDCDDC
I aligned this fastq file with a reference genome using bowtie. How can I identify the sample name from this record?
I have demultiplexed fastq files for each sample and I also have barcode information file in the format
sample name Index sequence BC1 CGATGT BC2 CGATGA
When I try to retrieve the alignment information using $sam->features() the seqID will be returned as
How can I get the 1:N:0:CGATGT part from the alignment information?