I have some samples with low mapping in Salmon (40% and less) that have higher alignments in Tophat, and trying to troubleshoot.
I picked some of the unmapped reads (from writeunmapped salmon parameter) and Blat them to human.
Some have 2 or more matches with identity 99% to 100% And some have many many matches, I need to scroll the page down too much. Many of these matches are 100% and some range between 85% to 100% identity.
I looked also into the “ambig_info.tsv’ , found some records with 0 unique mapping and more than 100 ambiguous mapping, but couldn’t relate to those unmapped.
This is how one match of one of them look in one mate and the other:
ACTIONS QUERY SCORE START END QSIZE IDENTITY CHRO STRAND START END SPAN browser details YourSeq 22 100 122 151 100.0% 10 + 37378275 37378303 29 browser details YourSeq 22 52 74 151 100.0% 10 - 37378275 37378303 29
So why this is not counted as mapped for example? Any hint, clue?