Hello,
I tryed HiSAT2 instead of Salmon quant, but I got the same issue with the BAM files … I see that some people had similar problem in the past : HISAT2 error: Auto-detection
I tried the auto-detect function as advised in this post. A little green box with "XXXX"appear but nothing has changed with the BAM file : BAM file is 3.2GB, can’t visualize it and doesn’t work as input for ValidateSamFile or Samtool sort. I’m digging the FAQ, but any advice will help.
Thanks.