This might be a silly question, but I'm confused about the output of samtools view. When I execute:
samtools view 1_BirA_mm10.bam | head
The output is this:
HWI-M01495:10:000000000-A5BGC:1:2107:12480:27069 337 1 30503670150M chrY 20418997 0 TCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTTCTTCTTCTTCTTCTTC HAGC/CHGFFHGHFHGCAGA0G/CG0FG/HAHHGCHFHGGHHFC?GFHGGFGEEAHHFCGGGCGCHFHHHEHGFFHFHFHHG1FHHGCHGFFFFHHHG3HHGAFHHEEGGCFADHGHG2HGAHFDGCABGCF4BA4FGFBFFFFCAAA@A AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:150YT:Z:UU NH:i:20 CC:Z:= CP:i:174010380 HI:i:3
As I understand it, this is not the Sam format. The Sam format should look like it does here:
Since you can use samtools view to convert from bam to sam, I'm trying to understand why the output is not in the sam format? Can someone explain the obvious thing I am apparently missing?
samtools view 1_BirA_mm10.bam | head
The output is this:
HWI-M01495:10:000000000-A5BGC:1:2107:12480:27069 337 1 30503670150M chrY 20418997 0 TCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTTCTTCTTCTTCTTCTTC HAGC/CHGFFHGHFHGCAGA0G/CG0FG/HAHHGCHFHGGHHFC?GFHGGFGEEAHHFCGGGCGCHFHHHEHGFFHFHFHHG1FHHGCHGFFFFHHHG3HHGAFHHEEGGCFADHGHG2HGAHFDGCABGCF4BA4FGFBFFFFCAAA@A AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:150YT:Z:UU NH:i:20 CC:Z:= CP:i:174010380 HI:i:3
As I understand it, this is not the Sam format. The Sam format should look like it does here:
Since you can use samtools view to convert from bam to sam, I'm trying to understand why the output is not in the sam format? Can someone explain the obvious thing I am apparently missing?
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