gravatar for tanya_fiskur

2 hours ago by

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?



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