Counts all read zero after alignment?
I’m looking for some help because I just ran my alignment code last night for 12 RNAseq samples. After taking a look at the counts that were generated this morning, all of them are reading 0 for every gene. Oddly, here are the results in the terminal…
95887304 reads; of these: 95887304 (100.00%) were unpaired; of these: 2313614 (2.41%) aligned 0 times 76638154 (79.93%) aligned exactly 1 time 16935536 (17.66%) aligned >1 times 97.59% overall alignment rate [bam_sort_core] merging from 32 files and 16 in-memory blocks...
Seems like the code is working for alignment but giving odd counts. Anyone have any ideas where to look?
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