collapse_isoforms_by_sam ValueError: Unknown format code 'f' for object of type 'str' about cdna_cupcake

[Magdoll]

Hi @markopetek ,

Please sort using

sort -k 3,3 -k 4,4n all_sizes.quivered_hq_MPE_S1.fastq.sam >  all_sizes.quivered_hq_MPE_S1.fastq.sorted.sam

instead.

This way, all unmapped alignments will occur before the mapped alignments. The error message comes from it expecting all unmapped alignments to have been seen already.

Another way is to simply remove unmapped reads from the SAM file using samtools view -F 4 (see here: https://groups.google.com/forum/#!msg/smrt_isoseq/zssNwq0aA4c/9UqOU4V0DQAJ)

[markopetek]

OK, now it works 👍 . Seems like I had a typo when I first copied this command to the console and it returned an error. I thought then it has to be a samtools sort since I've done it so many times before 😄
Thanks for help.