I have few BAM files which are generated from Ion Torrent Server (ampliseq) aligned to hg19 genome. I want to extract read counts from the bam files and I know that "featureCounts" can be used for this. But before getting the read counts, to view the bam file I gave the following command:
samtools view -H IonXpress_input.bam
@HD VN:1.4 SO:coordinate GO:none @SQ SN:NR_039978 LN:984 @SQ SN:NM_130786 LN:1766 @SQ SN:NM_138932 LN:9293 @SQ SN:NM_033110 LN:2678 @SQ SN:NM_000014 LN:4678 @SQ SN:NM_144670 LN:5192 @SQ SN:NR_040112 LN:1201 @SQ SN:NM_017436 LN:2106 @SQ SN:NM_016161 LN:1771 @SQ SN:NM_015665 LN:1854
I guess these are from header. After these I see something like following:
@RG ID:JODXM.IonXpress_022.1 CN:S5TorrentServerVM/MT205524 DT:2017-12-07T12:04:52+0100 FO:TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGA KS:TCAGTTCGAGACGCGAT PG:tmap PL:IONTORRENT PU:s5/540/IonXpress_022 SM:SNU449_TEAD4
Haven't seen a bam file like this before. Any idea what are these and how I can get read counts?