Hi!
I would really appreciate any help.
My .sam file, obtained after mapping with minimap2, looks like this:
@HD VN:1.5 SO:coordinate pb:3.0.1
@SQ SN:sgr01 LN:98476147
@SQ SN:sgr02 LN:88342039
@SQ SN:sgr03 LN:76488725
@SQ SN:sgr04 LN:75030901
@SQ SN:sgr05 LN:70255127
(....)
And the test .sam file looks like this:
sample1_HQ_transcript/48 0 chr1 12230030 60 7M1D46M2I37M4070N169M1D3M8149N78M1655N75M1I116M100N81M4605N117M4382N105M2506N96M1I75M483N101M847N90M1I79M2589N102M153N202M751N68M1I1 M1159N134M2178N156M571N211M959N75M3867N207M1974N90M3307N141M2338N123M5955N1I9M1I94M1013N153M2322N91M1I45M1095N48M2170N151M190N211M4599N248M1677N192M307N127M1934N124M1I19M4118N131M221N176M5220N124M875N236M 4047N109M4569N36M1D127M896N109M3379N180M2104N114M811N150M13846N150M1277N97M2120N149M11113N135M1438N168M39170N133M4070N196M37103N58M1I74M9221N241M1799N548M * 0 0 CTGAGCGCGCGGGCCTGCGCCATTGAGGAGCGGCGGGGAGGAAACGCCGCGCAGCGCGCCGGGCTGGGGCGGGCGGCCCGGGACACCGACAGATTTTTCTGTGACCATGAAAGAGAGAAATAAAGAATGATCCATGATTTCTAAACACCTTTTCCTGAGGATATAGTCATGTTGGAAGGCCTTGTAGCCTGGGTTCTCAATACCTATTTGGGAAAATATGTCAATAACTGTGGAGAATATTGAATTAAAAATTCAAGATGTCC (....)
The command, that I try to use, works normally with the test file and doesn't work with mine.
Is it somehow possible to make my file have the same formatting as the test one?